6IPC

Non-native human ferritin 8-mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.443 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages.

Zang, J.Chen, H.Zhang, X.Zhang, C.Guo, J.Du, M.Zhao, G.

(2019) Nat Commun 10: 778-778

  • DOI: 10.1038/s41467-019-08788-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Constructing different protein nanostructures with high-order discrete architectures by using one single building block remains a challenge. Here, we present a simple, effective disulfide-mediated approach to prepare a set of protein nanocages with d ...

    Constructing different protein nanostructures with high-order discrete architectures by using one single building block remains a challenge. Here, we present a simple, effective disulfide-mediated approach to prepare a set of protein nanocages with different geometries from single building block. By genetically deleting an inherent intra-subunit disulfide bond, we can render the conversion of an 8-mer bowl-like protein architecture (NF-8) into a 24-mer ferritin-like nanocage in solution, while selective insertion of an inter-subunit disulfide bond into NF-8 triggers its conversion into a 16-mer lenticular nanocage. Deletion of the same intra-subunit disulfide bond and insertion of the inter-subunit disulfide bond results in the conversion of NF-8 into a 48-mer protein nanocage in solution. Thus, in the laboratory, simple mutation of one protein building block can generate three different protein nanocages in a manner that is highly reminiscent of natural pentamer building block originating from viral capsids that self-assemble into protein assemblies with different symmetries.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: chenzhongzhou@cau.edu.cn.,Center of Biomedical Analysis, Tsinghua University, 100084, Beijing, China.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas , Universidade Federal de Minas Gerais , Av. Antônio Carlos , 6627 Belo Horizonte , Brazil.,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, 116034, Dalian, China. duming@dlpu.edu.cn.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China. gzhao@cau.edu.cn.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 7990 Enterprise Street, Burnaby, BC V5A 1V7, Canada.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA. dlloyd@amgen.com.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Amgen Research, Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista , Rua Cristóvão Colombo , 2265 São José do Rio Preto , Brazil.,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Departamento de Microbiología, Facultad de Salud , Universidad del Valle , Calle 4B No. 36-00 Cali , Colombia.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.,Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Amgen Research, Comparative Biology and Safety Sciences, Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
A, B, C, E, F, G, H, I, J, K, M, N, O, P
176Homo sapiensMutation(s): 3 
Gene Names: FTH1 (FTH, FTHL6)
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Go to Gene View: FTH1
Go to UniProtKB:  P02794
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
D, L
176Homo sapiensMutation(s): 2 
Gene Names: FTH1 (FTH, FTHL6)
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Go to Gene View: FTH1
Go to UniProtKB:  P02794
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, K
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.443 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.304α = 90.10
b = 139.223β = 90.28
c = 139.114γ = 90.18
Software Package:
Software NamePurpose
HKL-3000data reduction
MOLREPphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaBX201700284

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release