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- PDB-2rsp: STRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS R... -

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Basic information

Entry
Database: PDB / ID: 2rsp
TitleSTRUCTURE OF THE ASPARTIC PROTEASE FROM ROUS SARCOMA RETROVIRUS REFINED AT 2 ANGSTROMS RESOLUTION
ComponentsRSV PROTEASE
KeywordsHYDROLASE(ASPARTYL PROTEINASE)
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / structural constituent of virion / nucleic acid binding / viral translational frameshifting / host cell plasma membrane ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / structural constituent of virion / nucleic acid binding / viral translational frameshifting / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic ...Retroviral Gag polyprotein, M / Retroviral M domain / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWlodawer, A. / Miller, M. / Jaskolski, M.
Citation
Journal: Biochemistry / Year: 1990
Title: Structure of the aspartic protease from Rous sarcoma retrovirus refined at 2-A resolution.
Authors: Jaskolski, M. / Miller, M. / Rao, J.K. / Leis, J. / Wlodawer, A.
#1: Journal: Nature / Year: 1989
Title: Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family
Authors: Miller, M. / Jaskolski, M. / Rao, J.K.M. / Leis, J. / Wlodawer, A.
History
DepositionOct 17, 1989Processing site: BNL
Revision 1.0Oct 17, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET (SHEET *INT* BELOW). SHEETS MA AND MB ARE EACH DISRUPTED BY BULGES AT RESIDUES ASP 78 IN STRAND 2 AND ARG 93 IN STRAND 3.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RSV PROTEASE
B: RSV PROTEASE


Theoretical massNumber of molelcules
Total (without water)27,2522
Polymers27,2522
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-8 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.950, 88.950, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-451-

HOH

21B-452-

HOH

DetailsTHE ACTIVE ENZYME IS A DIMER COMPOSED OF TWO RSV PR MOLECULES. THIS DIMER COMPRISES THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE MOLECULES IN THIS DIMER ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS WHICH IS NEARLY COINCIDENT WITH THE (2 1 -3) CRYSTAL DIRECTION. CHAIN IDENTIFIERS *A* AND *B* HAVE BEEN ASSIGNED TO THE TWO MOLECULES PRESENTED IN THIS ENTRY.

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Components

#1: Protein RSV PROTEASE


Mass: 13625.862 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P03322
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTIC SITE IS FORMED BY TWO ASP-SER-GLY LOOPS, ONE FORM EACH SUBUNIT, CONNECTED BY AN ...THE CATALYTIC SITE IS FORMED BY TWO ASP-SER-GLY LOOPS, ONE FORM EACH SUBUNIT, CONNECTED BY AN INTRICATE SYSTEM OF HYDROGEN BONDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 20613 / % possible obs: 86 % / Observed criterion σ(I): 1.5 / Num. measured all: 95106 / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→10 Å
Details: THE SG ATOMS OF CYS A 113 AND CYS B 113 HAVE BEEN REFINED IN TWO ALTERNATE POSITIONS WITH AN OCCUPANCY OF 0.5 FOR EACH POSITION.
RfactorNum. reflection
obs0.144 17609
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 0 252 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0620.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0760.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2182
X-RAY DIFFRACTIONp_mcangle_it3.1442.5
X-RAY DIFFRACTIONp_scbond_it5.4443.5
X-RAY DIFFRACTIONp_scangle_it7.6124.5
X-RAY DIFFRACTIONp_plane_restr0.020.018
X-RAY DIFFRACTIONp_chiral_restr0.2250.15
X-RAY DIFFRACTIONp_singtor_nbd0.2020.3
X-RAY DIFFRACTIONp_multtor_nbd0.2140.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1910.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.43
X-RAY DIFFRACTIONp_staggered_tor16.910
X-RAY DIFFRACTIONp_orthonormal_tor39.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 17609 / Rfactor obs: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 2.2 Å

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