3MOB

Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 11 aa gp41 MPER-derived peptide

• PDB DOI: https://doi.org/10.2210/pdb3MOB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus type 1 group M subtype D (isolate Z6), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2010-04-22 Released: 2010-11-17 
• Deposition Author(s): Nicely, N.I., Dennison, S.M., Kelsoe, G., Liao, H.-X., Alam, S.M., Haynes, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.190 
• R-Value Observed: 0.195 

Literature

Crystal Structure of a Non-Neutralizing HIV-1 gp41 Envelope Antibody Demonstrates Neutralization Mechanism of gp41 Antibodies

Nicely, N.I., Dennison, S.M., Kelsoe, G., Ueda, Y., Liao, H.-X., Alam, S.M., Haynes, B.F.

To be published.

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: 49.94 kDa 
• Atom Count: 3,570 
• Modelled Residue Count: 458 
• Deposited Residue Count: 463 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41 MPER-derived peptide	A [auth P]	12	N/A	Mutation(s): 0
UniProt
Find proteins for P04580 (Human immunodeficiency virus type 1 group M subtype D (isolate Z6)) Explore P04580  Go to UniProtKB:  P04580

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN	C [auth H]	237	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.190 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.505	α = 90
b = 64.976	β = 90
c = 173.046	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Nicely, N.I., Dennison, S.M., Kelsoe, G., Liao, H.-X., Alam, S.M., Haynes, B.F.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description