4LSS

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade A strain KER_2018_11 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 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

  • DOI: 10.1016/j.immuni.2013.04.012
  • Primary Citation of Related Structures:  4LSP, 4LSQ, 4LSR, 4LST, 4LSU, 4LSV
  • Also Cited By: 4JPW

  • 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 m ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
envelope glycoprotein GP120
G
359Human immunodeficiency virus 1Gene Names: env
Find proteins for Q3ZLH8 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q3ZLH8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEAVY CHAIN OF ANTIBODY VRC01
H
224N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LIGHT CHAIN OF ANTIBODY VRC01 with N72T mutation
L
210N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
G, H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
G, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
G
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.639α = 90.00
b = 65.267β = 90.00
c = 259.146γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Database references
  • Version 1.3: 2014-05-07
    Type: Other
  • Version 1.4: 2017-11-15
    Type: Refinement description