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- PDB-1vsd: ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, ... -

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Basic information

Entry
Database: PDB / ID: 1vsd
TitleASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM
ComponentsINTEGRASE
KeywordsENDORIBONUCLEASE / HYDROLASE / ENDONUCLEASE
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 / Resolution: 1.7 Å
AuthorsBujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A.
CitationJournal: Structure / Year: 1996
Title: The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations.
Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M.
History
DepositionNov 29, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0303
Polymers16,7671
Non-polymers2632
Water3,117173
1
A: INTEGRASE
hetero molecules

A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0606
Polymers33,5352
Non-polymers5254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1930 Å2
ΔGint-21 kcal/mol
Surface area15120 Å2
Unit cell
Length a, b, c (Å)66.050, 66.050, 81.650
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
DetailsTHIS FILE CONTAINS ONLY A MONOMER. IN ORDER TO CREATE THE SECOND SUBUNIT OF THE DIMERIC MOLECULE, THE FRACTIONAL CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED BY Y, X, 1.0 - Z.

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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
Details: CRYSTALS SOAKED IN 500 MILLIMOLAR MGCL2
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., ...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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...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 "POL-RSVP" SEQUENCE DIFFERS AT TWO POSITIONS WITH THE CONSERVATIVE AMINO ACID RESIDUE DIFFERENCES NOTED (VAL -> ALA 101 AND ARG -> LYS 166).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growpH: 7.5
Details: pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLI-MOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 500 MILLI-MOLAR MGCL2.

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 30, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19297 / % possible obs: 99.8 % / Redundancy: 4.88 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→8 Å / σ(F): 2
Details: THE CLOSE (LESS THAN 2.5 ANGSTROMS) CONTACTS AT 146 ILE N - 148 ASN O (MAIN-MAIN) AND 149 ASN O - 151 GLN N (MAIN-MAIN) ARE LOCATED IN THE LEAST RELIABLE PART OF THE MODEL, A FLEXIBLE LOOP ...Details: THE CLOSE (LESS THAN 2.5 ANGSTROMS) CONTACTS AT 146 ILE N - 148 ASN O (MAIN-MAIN) AND 149 ASN O - 151 GLN N (MAIN-MAIN) ARE LOCATED IN THE LEAST RELIABLE PART OF THE MODEL, A FLEXIBLE LOOP REGION. THE QUALITY OF THE ELECTRON DENSITY AND THE RELATIVELY HIGHER B-FACTORS IN THIS SHORT SECTION OF THE SEQUENCE RESULTED IN POORER FINAL REFINEMENT THAN FOR THE REST OF THIS STRUCTURE.
RfactorNum. reflection% reflection
Rfree0.191 --
obs0.15 16330 91.6 %
Displacement parametersBiso mean: 27.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 16 173 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.053
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2382.5
X-RAY DIFFRACTIONp_mcangle_it3.6573.4
X-RAY DIFFRACTIONp_scbond_it5.0463.8
X-RAY DIFFRACTIONp_scangle_it7.7716.6
X-RAY DIFFRACTIONp_plane_restr0.0150.025
X-RAY DIFFRACTIONp_chiral_restr0.1360.18
X-RAY DIFFRACTIONp_singtor_nbd0.1910.4
X-RAY DIFFRACTIONp_multtor_nbd0.1670.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2480.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor33.6
X-RAY DIFFRACTIONp_staggered_tor15.610
X-RAY DIFFRACTIONp_orthonormal_tor37.410
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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