4RQS

Crystal structure of fully glycosylated HIV-1 gp120 core bound to CD4 and 17b Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.49 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262.

Kong, L.Wilson, I.A.Kwong, P.D.

(2015) Proteins 83: 590-596

  • DOI: 10.1002/prot.24747
  • Primary Citation of Related Structures:  
    4RQS

  • PubMed Abstract: 
  • The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc(2)Man(7) was modeled ...

    The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc(2)Man(7) was modeled. The GlcNAc stem of this glycan is largely buried in a cleft in gp120, suggesting a role in gp120 folding and stability. Its arms interact with the stems of neighboring glycans from the oligomannose patch, which is a major target for broadly neutralizing antibodies.


    Organizational Affiliation

    Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, 20892; Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, the Scripps Research Institute, La Jolla, California; Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, the Scripps Research Institute, La Jolla, California.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-domain CD4A [auth B]185Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
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Go to UniProtKB:  P01730
NIH Common Fund Data Resources
PHAROS:  P01730
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
17b Fab Light ChainB [auth C]214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
17b Fab Heavy ChainC [auth D]229Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 YU2 gp120 core chimeric proteinD [auth G]313Human immunodeficiency virus type 1 (isolate YU2)Mutation(s): 0 
Gene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35961 
Go to UniProtKB:  P35961
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth A]9 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth E], H, I, J2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth F], K, L3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth G]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.49 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.279 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.318α = 90
b = 171.318β = 90
c = 151.857γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2017-06-28
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary