3MNW | pdb_00003mnw

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide in a helical conformation

• PDB DOI: https://doi.org/10.2210/pdb3MNW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Mus musculus, 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: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.8 kDa 
• Atom Count: 3,709 
• Modeled Residue Count: 440 
• Deposited Residue Count: 464 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gp41	A [auth P]	21	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN	B [auth A]	224	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0  Go to UniProtKB:  Q8TCD0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN	C [auth B]	219	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291  Go to UniProtKB:  S6B291

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.753	α = 90
b = 160.989	β = 90
c = 141.055	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: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary