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 
  • R-Value Work: 0.202 

Starting Models: experimental
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This is version 1.8 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
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  • Reference Sequence
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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
GTEx:  ENSG00000010610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01730
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-HIV-1 antibody 412d light chain
C, G
214Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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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
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  • 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]
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
OA [auth E],
P [auth A],
PA [auth E],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [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]
BA [auth C],
CA [auth C],
DA [auth D],
TA [auth E],
UA [auth E],
WA [auth F],
Z [auth A]
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 
  • R-Value Work: 0.202 
  • 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

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Ligand Structure Quality Assessment 


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