4J6R | pdb_00004j6r

Crystal structure of broadly and potently neutralizing antibody VRC23 in complex with HIV-1 gp120

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history. 

Literature

Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.

Georgiev, I.S., Doria-Rose, N.A., Zhou, T., Kwon, Y.D., Staupe, R.P., Moquin, S., Chuang, G.Y., Louder, M.K., Schmidt, S.D., Altae-Tran, H.R., Bailer, R.T., McKee, K., Nason, M., O'Dell, S., Ofek, G., Pancera, M., Srivatsan, S., Shapiro, L., Connors, M., Migueles, S.A., Morris, L., Nishimura, Y., Martin, M.A., Mascola, J.R., Kwong, P.D.

(2013) Science 340: 751-756

  • DOI: https://doi.org/10.1126/science.1233989
  • Primary Citation Related Structures: 
    4J6R, 4JB9

  • PubMed Abstract: 

    Serum characterization and antibody isolation are transforming our understanding of the humoral immune response to viral infection. Here, we show that epitope specificities of HIV-1-neutralizing antibodies in serum can be elucidated from the serum pattern of neutralization against a diverse panel of HIV-1 isolates. We determined "neutralization fingerprints" for 30 neutralizing antibodies on a panel of 34 diverse HIV-1 strains and showed that similarity in neutralization fingerprint correlated with similarity in epitope. We used these fingerprints to delineate specificities of polyclonal sera from 24 HIV-1-infected donors and a chimeric siman-human immunodeficiency virus-infected macaque. Delineated specificities matched published specificities and were further confirmed by antibody isolation for two sera. Patterns of virus-isolate neutralization can thus afford a detailed epitope-specific understanding of neutralizing-antibody responses to viral infection.

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

Macromolecule Content 

  • Total Structure Weight: 90.6 kDa 
  • Atom Count: 7,245 
  • Modeled Residue Count: 775 
  • Deposited Residue Count: 793 
  • Unique protein chains: 3

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A [auth G]359Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q8J581 (Human immunodeficiency virus type 1)
Explore Q8J581 
Go to UniProtKB:  Q8J581
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J581
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAVY CHAIN OF ANTIBODY VRC23B [auth H]224Homo sapiensMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LIGHT CHAIN OF ANTIBODY VRC23C [auth L]210Homo sapiensMutation(s): 0 

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
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
TRS

Query on TRS


Download:Ideal Coordinates CCD File
AA [auth H]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD

Query on MPD


Download:Ideal Coordinates CCD File
R [auth H](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
BU3

Query on BU3


Download:Ideal Coordinates CCD File
FA [auth L](R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
CA [auth L]
DA [auth L]
EA [auth L]
N [auth G]
O [auth G]
CA [auth L],
DA [auth L],
EA [auth L],
N [auth G],
O [auth G],
P [auth G],
Q [auth G],
S [auth H],
T [auth H],
U [auth H],
V [auth H],
W [auth H],
X [auth H],
Y [auth H],
Z [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
BA [auth L],
M [auth G]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA		B [auth H]L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.044α = 90
b = 68.692β = 90
c = 214.534γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • 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: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-10-16
    Changes: Structure summary