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- PDB-1a5x: ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 -

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Basic information

Entry
Database: PDB / ID: 1a5x
TitleASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3
ComponentsINTEGRASE
KeywordsHYDROLASE / ENDONUCLEASE / HIV-1 INTEGRASE INHIBITOR
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
Chem-Y3 / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor.
Authors: Lubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A. / Zhao, H. / Burke Jr., T.R. / Neamati, N. / Pommier, Y. / Merkel, G. / Skalka, A.M.
History
DepositionFeb 18, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,7602
Polymers17,3991
Non-polymers3611
Water3,045169
1
A: INTEGRASE
hetero molecules

A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5214
Polymers34,7982
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)66.443, 66.443, 81.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE AUTHOR MAINTAINS THAT THE BIOLOGICAL UNIT IS NOT YET KNOWN. THE MINIMUM MULTIMER IS BELIEVED TO CONTAIN AT LEAST THE DIMER GENERATED BT THE TRANSFORMATION IN REMARK 350, SHOWN IN BOTH HIV-1 AND ASV INTEGRASE CORE DOMAIN STRUCTURES.

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Components

#1: Protein INTEGRASE


Mass: 17398.922 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
Details: P03354 FRAGMENT OF POLYPROTEIN POL-RSVP
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin)
Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / Description: SEE JRNL REFERENCE / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli)
References: UniProt: P03354, UniProt: O92956*PLUS, RNA-directed DNA polymerase
#2: Chemical ChemComp-Y3 / 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID


Mass: 361.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO8S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5 / Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1M HEPES, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-7.5 mg/mlprotein1drop
2100 mMHEPES1reservoir
310 %isopropanol1reservoir
50.1 Minhibitor1drop
4PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 17, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 14942 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.72 % / Rsym value: 0.058 / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.373 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 115637 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ASV

1asv


Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
Details: ATOMIC OCCUPANCIES OF DISORDERED ATOMS ARE SET TO 0.00 IN THE COORDINATES.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1351 10 %RANDOM
Rwork0.155 ---
obs0.155 13681 93.3 %-
Displacement parametersBiso mean: 30.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 23 169 1322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2252 163 10 %
Rwork0.2112 1326 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_FY.PROTOPHCSDX_FY.PRO
X-RAY DIFFRACTION2PARAM_SIMPLE.INHIBITORTOPH_SIMPLE.INHIBITOR
X-RAY DIFFRACTION3PARAM19.SOLVTOPH19.SOLV
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.99
LS refinement shell
*PLUS
Rfactor obs: 0.2112

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