4LSU | pdb_00004lsu

Crystal structure of broadly and potently neutralizing antibody VRC-PG20 in complex with HIV-1 clade A/E 93TH057 gp120

PDB DOI: https://doi.org/10.2210/pdb4LSU/pdb

Classification: viral protein/immune system
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-07-23 Released: 2013-08-21
Deposition Author(s): Zhou, T., Moquin, S., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.

Zhou, T., Zhu, J., Wu, X., Moquin, S., Zhang, B., Acharya, P., Georgiev, I.S., Altae-Tran, H.R., Chuang, G.Y., Joyce, M.G., Do Kwon, Y., Longo, N.S., Louder, M.K., Luongo, T., McKee, K., Schramm, C.A., Skinner, J., Yang, Y., Yang, Z., Zhang, Z., Zheng, A., Bonsignori, M., Haynes, B.F., Scheid, J.F., Nussenzweig, M.C., Simek, M., Burton, D.R., Koff, W.C., Mullikin, J.C., Connors, M., Shapiro, L., Nabel, G.J., Mascola, J.R., Kwong, P.D.

(2013) Immunity 39: 245-258

PubMed: 23911655 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.immuni.2013.04.012
Primary Citation Related Structures:
4LSP, 4LSQ, 4LSR, 4LSS, 4LST, 4LSU, 4LSV

PubMed Abstract:
Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain. Here we determine the ontogeny of the VRC01 class by crystallography and next-generation sequencing. Despite antibody-sequence differences exceeding 50%, antibody-gp120 cocrystal structures reveal VRC01-class recognition to be remarkably similar. B cell transcripts indicate that VRC01-class antibodies require few specific genetic elements, suggesting that naive-B cells with VRC01-class features are generated regularly by recombination. Virtually all of these fail to mature, however, with only a few-likely one-ancestor B cell expanding to form a VRC01-class lineage in each donor. Developmental similarities in multiple donors thus reveal the generation of VRC01-class antibodies to be reproducible in principle, thereby providing a framework for attempts to elicit similar antibodies in the general population.

Organizational Affiliation

Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 88.85 kDa
Atom Count: 6,365
Modeled Residue Count: 771
Deposited Residue Count: 784
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 CLADE A/E STRAIN 93TH057 GP120	A [auth G]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0ED31
Glycosylation
Glycosylation Sites: 10	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 OF ANTIBODY VRC-PG20	B [auth H]	227	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF ANTIBODY VRC-PG20	C [auth L]	204	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth G] MOL2 format, chain N [auth G] mmCIF format, chain N [auth G]	N [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain N [auth G] Interactions & Density Focus chain N [auth G]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth G] SDF format, chain L [auth G] SDF format, chain K [auth G] SDF format, chain J [auth G] SDF format, chain I [auth G] SDF format, chain H [auth G] SDF format, chain G SDF format, chain F [auth G] SDF format, chain E [auth G] SDF format, chain D [auth G] MOL2 format, chain M [auth G] MOL2 format, chain L [auth G] MOL2 format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain I [auth G] MOL2 format, chain H [auth G] MOL2 format, chain G MOL2 format, chain F [auth G] MOL2 format, chain E [auth G] MOL2 format, chain D [auth G] mmCIF format, chain M [auth G] mmCIF format, chain L [auth G] mmCIF format, chain K [auth G] mmCIF format, chain J [auth G] mmCIF format, chain I [auth G] mmCIF format, chain H [auth G] mmCIF format, chain G mmCIF format, chain F [auth G] mmCIF format, chain E [auth G] mmCIF format, chain D [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], M [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] Focus chain M [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] Focus chain M [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth L] SDF format, chain R [auth H] SDF format, chain Q [auth H] SDF format, chain P [auth G] SDF format, chain O [auth G] MOL2 format, chain T [auth L] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth G] MOL2 format, chain O [auth G] mmCIF format, chain T [auth L] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth G] mmCIF format, chain O [auth G]	O [auth G], P [auth G], Q [auth H], R [auth H], T [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth H] Focus chain T [auth L] Interactions & Density Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth H] Focus chain T [auth L]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth H] MOL2 format, chain S [auth H] mmCIF format, chain S [auth H]	S [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth H] Interactions & Density Focus chain S [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth H]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.234 (Depositor), 0.237 (DCC)
R-Value Work: 0.179 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.283	α = 90
b = 66.313	β = 108.34
c = 95.108	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Zhou, T.

Moquin, S.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references
Version 1.2: 2013-09-25
Changes: Database references
Version 1.3: 2014-05-07
Changes: Other
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2024-10-30
Changes: Data collection, Database references, Structure summary