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- PDB-1vsh: ASV INTEGRASE CORE DOMAIN WITH ZN(II) COFACTORS -

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Basic information

Entry
Database: PDB / ID: 1vsh
TitleASV INTEGRASE CORE DOMAIN WITH ZN(II) COFACTORS
ComponentsINTEGRASE
KeywordsENDONUCLEASE / HYDROLASE / ENDORIBONUCLEASE / RNA-DIRECTED DNA POLYMERASE
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / 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 / DNA integration / viral genome integration into host DNA / virion component / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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 speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / ISOSTRUCTURAL TO PDB ENTRY 1VSF / Resolution: 1.95 Å
AuthorsBujacz, G. / Alexandratos, J. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity.
Authors: Bujacz, G. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Andrake, M. / Katz, R.A. / Skalka, A.M.
History
DepositionMar 4, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2676
Polymers16,7671
Non-polymers5005
Water2,360131
1
A: INTEGRASE
hetero molecules

A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,53412
Polymers33,5352
Non-polymers1,00010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3350 Å2
ΔGint-258 kcal/mol
Surface area14070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.080, 66.080, 80.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER.

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Components

#1: Protein INTEGRASE


Mass: 16767.285 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin)
Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin
Description: 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. ...Description: 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).
Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES REFERENCE: THE APPARENT ...ALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES REFERENCE: THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE POL_RSVP SEQUENCE IS A RESULT OF VIRAL STRAIN VARIATION. THE STRAIN USED FOR THIS WORK, ROUS SARCOMA VIRUS SCHMIDT-RUPPIN B, COMPARED TO THE POL-RSVP SEQUENCE DIFFERS AT TWO POSITIONS WITH THE CONSERVATIVE AMINO ACID RESIDUE DIFFERENCES VAL -> ALA 101, ARG -> LYS 166.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM ZNCL2.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG40001reservoir
2100 mMHEPES1reservoir
310 %isopropanol1reservoir
46-7.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 13238 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.087 / Net I/σ(I): 13.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.424 / % possible all: 94.7

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Processing

Software
NameClassification
PROFFTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOSTRUCTURAL TO PDB ENTRY 1VSF
Resolution: 1.95→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.173 --
obs-12082 97 %
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 19 131 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.053
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4352.5
X-RAY DIFFRACTIONp_mcangle_it3.9633.4
X-RAY DIFFRACTIONp_scbond_it5.0433.8
X-RAY DIFFRACTIONp_scangle_it7.5236.6
X-RAY DIFFRACTIONp_plane_restr0.0160.025
X-RAY DIFFRACTIONp_chiral_restr0.1740.18
X-RAY DIFFRACTIONp_singtor_nbd0.1970.4
X-RAY DIFFRACTIONp_multtor_nbd0.2380.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2320.4
X-RAY DIFFRACTIONp_planar_tor2.83.6
X-RAY DIFFRACTIONp_staggered_tor18.410
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.710
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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