4YFL | pdb_00004yfl

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 gp120

• PDB DOI: https://doi.org/10.2210/pdb4YFL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-02-25 Released: 2015-06-03 
• Deposition Author(s): Acharya, P., Zhou, T., Moquin, S., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 
  0.326 (Depositor) 
• R-Value Work: 
  0.268 (Depositor) 
• R-Value Observed: 
  0.275 (Depositor) 

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, 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 
• 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.

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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: [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases and National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 176.2 kDa 
• Atom Count: 12,046 
• Modeled Residue Count: 1,547 
• Deposited Residue Count: 1,590 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160	A [auth G], D [auth E]	353	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus type 1) Explore Q0ED31  Go to UniProtKB:  Q0ED31
Glycosylation
Glycosylation Sites: 6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1B2530 heavy chain	B [auth H], E [auth F]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1B2530 Light chain	C [auth L], F [auth I]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth E], R [auth E], S [auth E], T [auth E], U [auth E], V [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free:  0.326 (Depositor) 
• R-Value Work:  0.268 (Depositor) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.962	α = 90
b = 57.318	β = 90.11
c = 254.715	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Acharya, P., Zhou, T., Moquin, S., Kwong, P.D.

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

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Database references
• Version 1.2: 2015-06-17
  Changes: Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary