4YE4 | pdb_00004ye4

Crystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120

PDB DOI: https://doi.org/10.2210/pdb4YE4/pdb

Classification: Viral protein/Immune system
Organism(s): Human immunodeficiency virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-02-23 Released: 2015-07-22
Deposition Author(s): Kwong, P.D., Chen, L., Zhou, T.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.187 (Depositor), 0.196 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.

Zhou, T., Lynch, R.M., Chen, L., Acharya, P., Wu, X., Doria-Rose, N.A., Joyce, M.G., Lingwood, D., Soto, C., Bailer, R.T., Ernandes, M.J., Kong, R., Longo, N.S., Louder, M.K., McKee, K., O'Dell, S., Schmidt, S.D., Tran, L., Yang, Z., Druz, A., Luongo, T.S., Moquin, S., Srivatsan, S., Yang, Y., Zhang, B., Zheng, A., Pancera, M., Kirys, T., Georgiev, I.S., Gindin, T., Peng, H.P., Yang, A.S., Mullikin, J.C., Gray, M.D., Stamatatos, L., Burton, D.R., Koff, W.C., Cohen, M.S., Haynes, B.F., Casazza, J.P., Connors, M., Corti, D., Lanzavecchia, A., Sattentau, Q.J., Weiss, R.A., West Jr., A.P., Bjorkman, P.J., Scheid, J.F., Nussenzweig, M.C., Shapiro, L., Mascola, J.R., Kwong, P.D.

(2015) Cell 161: 1280-1292

PubMed: 26004070 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2015.05.007
Primary Citation Related Structures:
4RWY, 4RX4, 4YDI, 4YDJ, 4YDK, 4YDL, 4YE4, 4YFL

PubMed Abstract:
The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA.

Department of Biochemistry & Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA.

Genomics Research Center, Academia Sinica, and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 11221.

NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02142, USA.

International AIDS Vaccine Initiative, New York, NY 10038, USA.

Departments of Medicine, Epidemiology, Microbiology, and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Duke University Human Vaccine Institute, Departments of Medicine, Surgery, Pediatrics, and Immunology, Duke University School of Medicine and the Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA.

HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA.

Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland; Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.

Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.

Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, UK.

Division of Infection & Immunity, University College London, Gower Street, London WC1E 6BT, UK.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.

Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry & Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: jmascola@nih.gov.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: pdkwong@nih.gov.

Macromolecule Content

Total Structure Weight: 90.07 kDa
Atom Count: 6,166
Modeled Residue Count: 778
Deposited Residue Count: 802
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HT593.1 gp120	A [auth G]	356	Human immunodeficiency virus	Mutation(s): 0
UniProt
Find proteins for Q69994 (Human immunodeficiency virus type 1) Explore Q69994 Go to UniProtKB: Q69994
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q69994
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain human antibody HJ16	B [auth H]	228	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of HJ16	C [auth L]	218	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth G] SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain D [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] mmCIF format, chain D [auth G] mmCIF format, chain E [auth G] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain I [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G]	D [auth G] E [auth G] F [auth G] G H [auth G] D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain D [auth G] Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.187 (Depositor), 0.196 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.712	α = 90
b = 99.037	β = 90
c = 180.426	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-22

Deposition Author(s):

Kwong, P.D.

Chen, L.

Zhou, T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-07-22
Type: Initial release
Version 1.1: 2015-10-07
Changes: Experimental preparation
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2020-03-04
Changes: Data collection, Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2022-03-30
Changes: Author supporting evidence, Database references, Structure summary
Version 1.6: 2024-11-13
Changes: Data collection, Structure summary