Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130830.13 
• Atom Count: 8313 
• Residue Count: 1176 
• Unique protein chains: 3

3U2S

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109

• DOI: 10.2210/pdb3U2S/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens


• Deposited: 2011-10-04 Released: 2011-11-30 
• Deposition Author(s): McLellan, J.S., Pancera, M., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.797 Å
• R-Value Free: 0.205 
• R-Value Work: 0.178 

Literature

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.

McLellan, J.S., Pancera, M., Carrico, C., Gorman, J., Julien, J.P., Khayat, R., Louder, R., Pejchal, R., Sastry, M., Dai, K., O'Dell, S., Patel, N., Shahzad-Ul-Hussan, S., Yang, Y., Zhang, B., Zhou, T., Zhu, J., Boyington, J.C., Chuang, G.Y., Diwanji, D., Georgiev, I., Do Kwon, Y., Lee, D., Louder, M.K., Moquin, S., Schmidt, S.D., Yang, Z.Y., Bonsignori, M., Crump, J.A., Kapiga, S.H., Sam, N.E., Haynes, B.F., Burton, D.R., Koff, W.C., Walker, L.M., Phogat, S., Wyatt, R., Orwenyo, J., Wang, L.X., Arthos, J., Bewley, C.A., Mascola, J.R., Nabel, G.J., Schief, W.R., Ward, A.B., Wilson, I.A., Kwong, P.D.

(2011) Nature 480: 336-343

• PubMed: 22113616 
• DOI: 10.1038/nature10696
• Primary Citation of Related Structures:  
  3U4E, 3U4B, 3U46, 3U36, 3U1S, 3TCL


• PubMed Abstract: 
  

Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PG9 heavy chain	H, A	248	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PG9 light chain	L, B	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp120	G, C	124	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q6TCP8 (Human immunodeficiency virus 1) Go to UniProtKB:  Q6TCP8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BU3	B, L	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N
SO4	B, H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MAN	C, G	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	C, G	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	C, G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, H	L-PEPTIDE LINKING	C5 H7 N O3		GLU
TYS	A, H	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.797 Å
• R-Value Free: 0.205 
• R-Value Work: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 89.465	α = 90.00
b = 86.565	β = 92.08
c = 94.879	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-04 
• Released Date: 2011-11-30 
• Deposition Author(s): McLellan, J.S., Pancera, M., Kwong, P.D.

Revision History 

• Version 1.0: 2011-11-30
  Type: Initial release
• Version 1.1: 2011-12-21
  Type: Database references