4RQS | pdb_00004rqs

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

• PDB DOI: https://doi.org/10.2210/pdb4RQS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus type 1 (isolate YU2)
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2014-11-05 Released: 2014-12-31 
• Deposition Author(s): Kong, L., Wilson, I.A., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.49 Å
• R-Value Free: 
  0.322 (Depositor), 0.339 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

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

• PubMed: 25546301 
• DOI: https://doi.org/10.1002/prot.24747
• Primary Citation 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.44 kDa 
• Atom Count: 7,379 
• Modeled Residue Count: 913 
• Deposited Residue Count: 941 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-domain CD4	A [auth B]	185	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
PHAROS:  P01730 GTEx:  ENSG00000010610

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
17b Fab Light Chain	B [auth C]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
17b Fab Heavy Chain	C [auth D]	229	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 YU2 gp120 core chimeric protein	D [auth G]	313	Human immunodeficiency virus type 1 (isolate YU2)	Mutation(s): 0
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961  Go to UniProtKB:  P35961
Glycosylation
Glycosylation Sites: 9

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	E [auth A]	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth E], H, I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F], K, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.49 Å
• R-Value Free:  0.322 (Depositor), 0.339 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.318	α = 90
b = 171.318	β = 90
c = 151.857	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Kong, L., Wilson, I.A., Kwong, P.D.

Revision History  

• 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
• Version 2.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary