3O3X | pdb_00003o3x

Crystal structure of gp41-5, a single-chain 5-helix-bundle based on HIV gp41

• PDB DOI: https://doi.org/10.2210/pdb3O3X/pdb

• Classification: VIRAL PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-26 Released: 2011-07-27 
• Deposition Author(s): Horne, W.S., Johnson, L.M., Gellman, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Broad Distribution of Energetically Important Contacts across an Extended Protein Interface.

Johnson, L.M., Horne, W.S., Gellman, S.H.

(2011) J Am Chem Soc 133: 10038-10041

• PubMed: 21644542 
• DOI: https://doi.org/10.1021/ja203358t
• Primary Citation Related Structures: 
  3O3X, 3O3Z, 3O40, 3O43


• PubMed Abstract: 
  

  Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble to form a core displaying long grooves that provide docking sites for three C-terminal heptad repeat (CHR) helices. We report experiments designed to discriminate between two alternative hypotheses regarding the source of affinity between individual CHR helices and the complementary groove: (1) affinity is dominated by interactions of a small cluster of side chains at one end of the CHR helix; or (2) affinity depends upon interactions distributed across the long CHR helix. We have employed two complementary experimental designs, and results from both favor the latter hypothesis.

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Organizational Affiliation: 
• Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 22.43 kDa 
• Atom Count: 1,883 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41-5	A	198	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.459	α = 90
b = 57.936	β = 90
c = 61.689	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Horne, W.S., Johnson, L.M., Gellman, S.H.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description