4JB9

Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core

• PDB DOI: https://doi.org/10.2210/pdb4JB9/pdb

• Classification: viral protein/immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-02-19 Released: 2013-05-08 
• Deposition Author(s): Kwon, Y.D., Zhou, T., Srivatsan, S., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.8 kDa 
• Atom Count: 6,237 
• Modelled Residue Count: 778 
• Deposited Residue Count: 794 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clade A/E 93TH057 HIV-1 gp120 core	A [auth G]	353	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1) Explore Q0ED31  Go to UniProtKB:  Q0ED31

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody VRC06 heavy chain	B [auth H]	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody VRC06 light chain	C [auth L]	209	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.244	α = 90
b = 68.924	β = 90
c = 224.225	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Kwon, Y.D., Zhou, T., Srivatsan, S., Kwong, P.D.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2016-10-19
  Changes: Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary