1M9C | pdb_00001m9c

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex.

• PDB DOI: https://doi.org/10.2210/pdb1M9C/pdb

• Classification: Isomerase/Viral protein
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-07-28 Released: 2003-05-27 
• Deposition Author(s): Howard, B.R., Vajdos, F.F., Li, S., Sundquist, W.I., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the catalytic mechanism of cyclophilin A

Howard, B.R., Vajdos, F.F., Li, S., Sundquist, W.I., Hill, C.P.

(2003) Nat Struct Biol 10: 475-481

• PubMed: 12730686 
• DOI: https://doi.org/10.1038/nsb927
• Primary Citation Related Structures: 
  1M9C, 1M9D, 1M9E, 1M9F, 1M9X, 1M9Y


• PubMed Abstract: 
  

  Cyclophilins constitute a ubiquitous protein family whose functions include protein folding, transport and signaling. They possess both sequence-specific binding and proline cis-trans isomerase activities, as exemplified by the interaction between cyclophilin A (CypA) and the HIV-1 CA protein. Here, we report crystal structures of CypA in complex with HIV-1 CA protein variants that bind preferentially with the substrate proline residue in either the cis or the trans conformation. Cis- and trans-Pro substrates are accommodated within the enzyme active site by rearrangement of their N-terminal residues and with minimal distortions in the path of the main chain. CypA Arg55 guanidinium group probably facilitates catalysis by anchoring the substrate proline oxygen and stabilizing sp3 hybridization of the proline nitrogen in the transition state.

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Organizational Affiliation: 
• Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.48 kDa 
• Atom Count: 4,856 
• Modeled Residue Count: 610 
• Deposited Residue Count: 622 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclophilin A	A, B	165	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Capsid	C, D	146	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q72497 (Human immunodeficiency virus type 1) Explore Q72497  Go to UniProtKB:  Q72497

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.445	α = 90
b = 113.235	β = 100.53
c = 67.006	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-27 
Deposition Author(s): Howard, B.R., Vajdos, F.F., Li, S., Sundquist, W.I., Hill, C.P.

Revision History  

• Version 1.0: 2003-05-27
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Refinement description