4XNZ

Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 gp120

• PDB DOI: https://doi.org/10.2210/pdb4XNZ/pdb

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


• Deposited: 2015-01-16 Released: 2015-04-29 
• Deposition Author(s): Zhou, T., Srivatsan, S., Kwong, P.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.301 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 268.18 kDa 
• Atom Count: 18,134 
• Modelled Residue Count: 2,294 
• Deposited Residue Count: 2,388 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160,Envelope glycoprotein gp160	A [auth G], D [auth A], G [auth D]	353	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
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
HEAVY CHAIN OF ANTIBODY VRC06B	B [auth H], E [auth B], H [auth E]	234	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF ANTIBODY VRC06B	C [auth L], F [auth C], I [auth F]	209	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], K [auth J], L [auth K]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], BA [auth D], CA [auth D], DA [auth D], M [auth G], N [auth G], O [auth G], P [auth G], Q [auth G], R [auth G], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.301 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.314	α = 90
b = 189.442	β = 90
c = 219.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Zhou, T., Srivatsan, S., Kwong, P.D.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary