4U6G | pdb_00004u6g

Crystal structure of 10E8 Fab in complex with a hydrocarbon-stapled HIV-1 gp41 MPER peptide

• PDB DOI: https://doi.org/10.2210/pdb4U6G/pdb

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


• Deposited: 2014-07-28 Released: 2014-12-03 
• Deposition Author(s): Ofek, G., Bird, G.H., Walensky, L.D., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structural Fidelity and Neutralizing Antibody Binding Capacity of Hydrocarbon-Stapled HIV-1 Antigens

Bird, G.H., Irimia, A., Ofek, G., Kwong, P.D., Wilson, I.A., Walensky, L.D.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.26 kDa 
• Atom Count: 7,020 
• Modeled Residue Count: 921 
• Deposited Residue Count: 936 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
10E8 Fab Heavy Chain	A [auth H], C [auth A]	236	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10E8 Fab Light Chain	B [auth L], D [auth B]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SAH-MPER(662-683KKK)(B,q)	E [auth P], F [auth C]	17	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for I3VHW6 (Human immunodeficiency virus type 1) Explore I3VHW6  Go to UniProtKB:  I3VHW6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DIV	E [auth P], F [auth C]	D-PEPTIDE LINKING	C5 H11 N O2		--
MK8	E [auth P], F [auth C]	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.562	α = 90
b = 126.317	β = 90
c = 129.875	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Ofek, G., Bird, G.H., Walensky, L.D., Kwong, P.D.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description