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.

Macromolecule Content

• Total Structure Weight: 106.4 kDa 
• Atom Count: 7,714 
• Modelled Residue Count: 930 
• Deposited Residue Count: 941 
• Unique protein chains: 4

 1G9N

HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

• PDB DOI: 10.2210/pdb1G9N/pdb

• Classification: Viral protein/Immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Drosophila melanogaster, Cricetulus griseus, Mus musculus
• Mutation(s): Yes 


• Deposited: 2000-11-25 Released: 2000-12-27 
• Deposition Author(s): Kwong, P.D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.207 

Literature

Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.

Kwong, P.D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

(2000) Structure 8: 1329-1339

• PubMed: 11188697 
• DOI: 10.1016/s0969-2126(00)00547-5
• Primary Citation of Related Structures:  
  1G9M, 1G9N


• PubMed Abstract: 
  

The gp120 exterior envelope glycoprotein of HIV-1 binds sequentially to CD4 and chemokine receptors on cells to initiate virus entry. During natural infection, gp120 is a primary target of the humoral immune response, and it has evolved to resist antibody-mediated neutralization. We previously reported the structure at 2.5 A of a gp120 core from the HXBc2 laboratory-adapted isolate in complex with a 2 domain fragment of CD4 and the antigen binding fragment of a human antibody. This revealed atomic details of gp120-receptor interactions and suggested multiple mechanisms of immune evasion.

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Related Citations: 

• Structure of an HIV GP120 Envelope Glycoprotein in Complex with the CD4 Receptor and a Neutralizing Human Antibody
  Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.
  (1998) Nature 393: 648

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN GP120	A [auth G]	313	Human immunodeficiency virus 1	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL SURFACE GLYCOPROTEIN CD4	B [auth C]	185	Homo sapiens	Mutation(s): 2  Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
PHAROS:  P01730

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY 17B, LIGHT CHAIN	C [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY 17B, HEAVY CHAIN	D [auth H]	229	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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], Q [auth G], R [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: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.98	α = 90
b = 81.71	β = 90.37
c = 74.48	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-27 
Deposition Author(s): Kwong, P.D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

Revision History  

• Version 1.0: 2000-12-27
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-02
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-27
  Changes: Advisory, Database references, Structure summary