6C5K

S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude.

Haji-Ghassemi, O.Muller-Loennies, S.Brooks, C.L.MacKenzie, C.R.Caveney, N.Van Petegem, F.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2019) Biochemistry 58: 714-726

  • DOI: 10.1021/acs.biochem.8b00318
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Murine antibodies S25-23, S25-26, and S25-5 derive from a common germ-line origin, and all bind the Chlamydiaceae family-specific epitope αKdo(2→8)αKdo(2→4)αKdo (where Kdo is 3-deoxy-α-d- manno-oct-2-ulosonic acid) with high affinity and specificity. ...

    Murine antibodies S25-23, S25-26, and S25-5 derive from a common germ-line origin, and all bind the Chlamydiaceae family-specific epitope αKdo(2→8)αKdo(2→4)αKdo (where Kdo is 3-deoxy-α-d- manno-oct-2-ulosonic acid) with high affinity and specificity. These antibodies recognize the entire trisaccharide antigen in a linkage-dependent manner via a groove composed largely of germ-line residues. Despite sharing identical heavy and light chain genes, S25-23 binds the family-specific epitope with nanomolar affinity, which is an order of magnitude higher than that of S25-26, while S25-5 displays an affinity between those of S25-23 and S25-26. We determined the high-resolution crystal structures of S25-23 and S25-5 antigen binding fragments in complex with a pentasaccharide derived from the LPS of Chlamydia and measured the affinity of S25-5 for chlamydial LPS antigens using isothermal titration microcalorimetry. The 1.75 Å resolution structure of S25-23 shows how subtle conservative mutations Arg(L)-27E to lysine and Ser(H)-56 to threonine lead to an order of magnitude increase in affinity. Importantly, comparison between previous S25-26 structures and the 1.99 and 2.05 Å resolution liganded and unliganded structures of S25-5, respectively, shows how a Ser(L)-27E mutation results in an intermediate affinity due to the reduced enthalpic penalty associated with complex formation that would otherwise be required for arginine in this position. This strategy allows for subtle adjustments in the combining site via affinity maturation that have dramatic consequences for the affinity of an antibody for its antigen.


    Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. Dorien.VanLysebetten@UGent.be.,The RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sato-gun, Hyogo, 678-5248, Japan.,Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China. Electronic address: hejin@mail.hzau.edu.cn.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.).,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. jeffreym@uow.edu.au.,Cambridge Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge, CB3 OFA, UK.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. lijunliuks@gmail.com.,Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy. massimo.bellanda@unipd.it.,Human Health Therapeutics Portfolio , National Research Council Canada , 100 Sussex Drive , Ottawa , Ontario , Canada K1A 0R6.,IGF, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,DLX Scientific, Lawrence, KS, USA. lijunliuks@gmail.com.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. t.durek@uq.edu.au.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China. Electronic address: zoutingting@mail.hzau.edu.cn.,Department of Pharmaceutical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.,Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. d.craik@imb.uq.edu.au.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA. xiaokun.shu@ucsf.edu.,Research Center Borstel , Leibniz Lung Center , Parkallee 22 , Borstel D-23845 , Germany.,IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , United States.,Biological Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain.,Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,From the Institute for Protein Design.,Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , California 94158 , United States.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Igua 4425, 11400, Montevideo, Uruguay.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy. stefania.abbruzzetti@unipr.it.,Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. xiaokun.shu@ucsf.edu.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan.,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. masato.noguchi@jt.com.,Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. djadams@uow.edu.au.,From the Institute for Protein Design, chris.bahl@proteininnovation.org.,the Institute for Protein Innovation, Boston, Massachusetts 02115.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. thomas.dash@imb.uq.edu.au.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France. Electronic address: gilles.labesse@cbs.cnrs.fr.,Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.,Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. rfinolu@uow.edu.au.,Department of Chemistry , Fresno State University , 2555 East San Ramon Avenue, MS SB70 , Fresno , California 93740 , United States.,Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States.,Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. peta.harvey@imb.uq.edu.au.,Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan.,Department of Chemistry , Box H, Brown University , Providence , Rhode Island 02912-9108 , United States.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.,Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain. fjluque@ub.edu.,Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.) augen-pioszak@ouhsc.edu.,School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK. robert.ford@manchester.ac.uk.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,Institute of Low Temperature Science, Hokkaido University Kita19-Nishi8, Kita-ku, 060-0819, Sapporo, Japan.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France. Electronic address: serge.roche@crbm.cnrs.fr.,School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. nyoman.kurniawan@cai.uq.edu.au.,Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, and.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy. cristiano.viappiani@unipr.it.,Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. justine.hill1@gmail.com.,Fundación ARAID, 50018, Zaragoza, Spain.,Department of Chemistry , University of Natural Resources and Life Sciences , A-1190 Vienna , Austria.,Department of Biochemistry, and.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,eBIC, Diamond Light Source Ltd, Diamond House, Harwell Science & Innovation Campus, Oxfordshire, Didcot, OX11 0DE, UK.,Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,University of Chinese Academy of Sciences, Beijing, 101408, China.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. tsuyoshi.adachi@jt.com.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA.,New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.,Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark.,Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy.,the Structural Biology Program and.,Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6.,Orphagen Pharmaceuticals, 11558 Sorrento Valley Road, Suite 4, San Diego, California, 92121, USA.,UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.,Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain.,Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei 430070, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG1 Fab Heavy Chain
H, A
218Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q99LC4 (Mus musculus)
Go to UniProtKB:  Q99LC4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IgG1 Fab Light Chain (Kappa)
L, B
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Z9M
Query on Z9M

Download SDF File 
Download CCD File 
A, H
2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
 Ligand Interaction
KDO
Query on KDO

Download SDF File 
Download CCD File 
A, H
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
GP1
Query on GP1

Download SDF File 
Download CCD File 
A, H
GLUCOSAMINE 1-PHOSPHATE
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 171.649α = 90.00
b = 62.710β = 116.09
c = 107.071γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaDiscovery Grant 171356-2013

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references