2QAD

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.269 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.210 (DCC) 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.9 of the entry. See complete history


Literature

Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4

Huang, C.-C.Lam, S.N.Acharya, P.Tang, M.Xiang, S.-H.Hussan, S.S.Stanfield, R.L.Robinson, J.Sodroski, J.Wilson, I.A.Wyatt, R.Bewley, C.A.Kwong, P.D.

(2007) Science 317: 1930-1934

  • DOI: https://doi.org/10.1126/science.1145373
  • Primary Citation of Related Structures:  
    2QAD, 2RLL

  • PubMed Abstract: 

    The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160
A, E
322Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35961 
Go to UniProtKB:  P35961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35961
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4
B, F
181Homo sapiensMutation(s): 0 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
PHAROS:  P01730
GTEx:  ENSG00000010610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01730
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-HIV-1 antibody 412d light chain
C, G
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
anti-HIV-1 antibody 412d heavy chain
D, H
231Homo sapiensMutation(s): 0 
UniProt
Find proteins for A4F255 (Homo sapiens)
Explore A4F255 
Go to UniProtKB:  A4F255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4F255
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth E]
FA [auth E]
GA [auth E]
HA [auth E]
I [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MLA
Query on MLA

Download Ideal Coordinates CCD File 
AA [auth B],
VA [auth F],
XA [auth H],
Y [auth A]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth D]
TA [auth E]
UA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
D, H
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.269 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.6α = 90
b = 53.021β = 104.64
c = 225.326γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AMoREphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.7: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2023-11-15
    Changes: Data collection
  • Version 1.9: 2024-11-20
    Changes: Structure summary