6XCJ

Crystal Structure of DH650 Fab from a Rhesus Macaque in Complex with HIV-1 gp120 Core

PDB DOI: https://doi.org/10.2210/pdb6XCJ/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-06-08 Released: 2020-12-02
Deposition Author(s): Raymond, D.D., Chug, H., Harrison, S.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.227
R-Value Observed: 0.230

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.

Roark, R.S., Li, H., Williams, W.B., Chug, H., Mason, R.D., Gorman, J., Wang, S., Lee, F.H., Rando, J., Bonsignori, M., Hwang, K.K., Saunders, K.O., Wiehe, K., Moody, M.A., Hraber, P.T., Wagh, K., Giorgi, E.E., Russell, R.M., Bibollet-Ruche, F., Liu, W., Connell, J., Smith, A.G., DeVoto, J., Murphy, A.I., Smith, J., Ding, W., Zhao, C., Chohan, N., Okumura, M., Rosario, C., Ding, Y., Lindemuth, E., Bauer, A.M., Bar, K.J., Ambrozak, D., Chao, C.W., Chuang, G.Y., Geng, H., Lin, B.C., Louder, M.K., Nguyen, R., Zhang, B., Lewis, M.G., Raymond, D.D., Doria-Rose, N.A., Schramm, C.A., Douek, D.C., Roederer, M., Kepler, T.B., Kelsoe, G., Mascola, J.R., Kwong, P.D., Korber, B.T., Harrison, S.C., Haynes, B.F., Hahn, B.H., Shaw, G.M.

(2021) Science 371

PubMed: 33214287 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.abd2638
Primary Citation of Related Structures:
6XCJ, 6XRT

PubMed Abstract:
Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.

Organizational Affiliation

Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content

Total Structure Weight: 90.13 kDa
Atom Count: 5,712
Modelled Residue Count: 721
Deposited Residue Count: 803
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope Glycoprotein gp120	A [auth G]	357	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for A0A0A7I3C6 (Human immunodeficiency virus 1) Explore A0A0A7I3C6 Go to UniProtKB: A0A0A7I3C6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A7I3C6
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH650 Fab Heavy Chain	B [auth H]	226	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH650 Fab Light Chain	C [auth L]	220	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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] SDF format, chain L [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] MOL2 format, chain L [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] mmCIF format, chain L [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], L [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] Focus chain L [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] Focus chain L [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.227
R-Value Observed: 0.230
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.52	α = 90
b = 122.1	β = 90
c = 53.4	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Raymond, D.D.

Chug, H.

Harrison, S.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI144371

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2021-01-20
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary