3D3T

Crystal Structure of HIV-1 CRF01_AE in complex with the substrate p1-p6

• PDB DOI: https://doi.org/10.2210/pdb3D3T/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1, Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)
• Expression System: Human immunodeficiency virus 1
• Mutation(s): Yes 


• Deposited: 2008-05-12 Released: 2008-07-08 
• Deposition Author(s): Bandaranayake, R.M., Prabu-Jeyabalan, M., Kakizawa, J., Sugiura, W., Schiffer, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 

Literature

Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6.

Bandaranayake, R.M., Prabu-Jeyabalan, M., Kakizawa, J., Sugiura, W., Schiffer, C.A.

(2008) J Virol 82: 6762-6766

• PubMed: 18434392 
• DOI: https://doi.org/10.1128/JVI.00018-08
• Primary Citation of Related Structures:  
  3D3T


• PubMed Abstract: 
  

  The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 22.79 kDa 
• Atom Count: 1,494 
• Modelled Residue Count: 206 
• Deposited Residue Count: 208 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for Q90VT5 (Human immunodeficiency virus type 1) Explore Q90VT5  Go to UniProtKB:  Q90VT5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P1-P6 SUBSTRATE PEPTIDE	C [auth P]	10	N/A	Mutation(s): 0
UniProt
Find proteins for P12495 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12495  Go to UniProtKB:  P12495

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.186	α = 90
b = 62.186	β = 90
c = 82.099	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Bandaranayake, R.M., Prabu-Jeyabalan, M., Kakizawa, J., Sugiura, W., Schiffer, C.A.

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2024-02-21
  Changes: Data collection