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- PDB-1asv: Avian sarcoma virus integrase catalytic core domain -

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Basic information

Entry
Database: PDB / ID: 1asv
TitleAvian sarcoma virus integrase catalytic core domain
ComponentsAVIAN SARCOMA VIRUS INTEGRASE
KeywordsDNA INTEGRATION
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesAvian sarcoma virus
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: High-resolution structure of the catalytic domain of avian sarcoma virus integrase.
Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M.
History
DepositionAug 25, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AVIAN SARCOMA VIRUS INTEGRASE


Theoretical massNumber of molelcules
Total (without water)17,9401
Polymers17,9401
Non-polymers00
Water2,108117
1
A: AVIAN SARCOMA VIRUS INTEGRASE

A: AVIAN SARCOMA VIRUS INTEGRASE


Theoretical massNumber of molelcules
Total (without water)35,8792
Polymers35,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1900 Å2
ΔGint-2.8 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.550, 66.550, 80.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 73

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Components

#1: Protein AVIAN SARCOMA VIRUS INTEGRASE


Mass: 17939.555 Da / Num. of mol.: 1
Mutation: INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209)
Source method: isolated from a genetically manipulated source
Details: CRYSTALLIZED FROM 20% PEG 4000, SODIUM CITRATE PH 5.6
Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN B / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Source detailsORIGINAL VIRAL DNA CLONE: JU ET AL., J. VIROL. 33:1026-1033 (1980) ORIGINAL EXPRESSION CLONE: TERRY ...ORIGINAL VIRAL DNA CLONE: JU ET AL., J. VIROL. 33:1026-1033 (1980) ORIGINAL EXPRESSION CLONE: TERRY ET AL., J. VIROL. 62:2358-2365 (1988) EXPRESSION CLONE FOR CORE: KULKOSKY ET AL., J. VIROL. 206:448-456 (1995)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
210 %isopropanol1reservoir
36-7.5 mg/mlprotein1drop
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 8, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 9620 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.93 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.234 --
obs0.142 7828 99.7 %
Displacement parametersBiso mean: 29.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 117 1240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.053
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3662.5
X-RAY DIFFRACTIONp_mcangle_it3.8973.5
X-RAY DIFFRACTIONp_scbond_it5.5593.8
X-RAY DIFFRACTIONp_scangle_it8.4546.6
X-RAY DIFFRACTIONp_plane_restr0.0150.025
X-RAY DIFFRACTIONp_chiral_restr0.1610.18
X-RAY DIFFRACTIONp_singtor_nbd0.2070.4
X-RAY DIFFRACTIONp_multtor_nbd0.2030.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2190.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.73.6
X-RAY DIFFRACTIONp_staggered_tor17.510
X-RAY DIFFRACTIONp_orthonormal_tor38.610
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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