4LSP | pdb_00004lsp

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.214 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.180 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.3 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: 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: 92.13 kDa 
  • Atom Count: 6,498 
  • Modeled Residue Count: 771 
  • Deposited Residue Count: 799 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 CLADE A/E STRAIN 93TH057 GP120A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus type 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Glycosylation
Glycosylation Sites: 12
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAVY CHAIN OF ANTIBODY VRC-CH31B [auth H]236Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LIGHT CHAIN OF ANTIBODY VRC-CH31C [auth L]210Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth G]
F [auth G]
G
H [auth G]
I [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],
N [auth G],
O [auth G],
P [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
X [auth G],
Y [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
HA [auth L],
Q [auth G],
R [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth H]
CA [auth H]
DA [auth H]
EA [auth H]
FA [auth H]
BA [auth H],
CA [auth H],
DA [auth H],
EA [auth H],
FA [auth H],
IA [auth L],
S [auth G],
T [auth G],
U [auth G],
V [auth G],
W [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth G],
GA [auth H],
Z [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.214 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.180 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.392α = 90
b = 83.958β = 90
c = 175.734γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2014-05-07
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-06-02
    Changes: Source and taxonomy, Structure summary
  • Version 2.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary