[English] 日本語
Yorodumi
- PDB-2x6n: Human foamy virus integrase - catalytic core. Manganese-bound str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x6n
TitleHuman foamy virus integrase - catalytic core. Manganese-bound structure.
ComponentsINTEGRASE
KeywordsVIRAL PROTEIN / RETROVIRAL INTEGRASE / DNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / DNA INTEGRATION / ASPARTYL PROTEASE / DNA RECOMBINATION / TRANSFERASE / NUCLEASE / HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell cytoplasm / viral entry into host cell / host cell nucleus / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
Foamy virus protease (FV PR) domain profile. / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase, C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / Ribonuclease H-like superfamily/Ribonuclease H ...Foamy virus protease (FV PR) domain profile. / Retroviral integrase C-terminal SH3 domain / Spumavirus aspartic protease A9 / Spumavirus aspartic protease (A9) / Retroviral integrase, C-terminal SH3 domain / Integrase zinc binding domain / Integrase zinc-binding domain / RNase H-like domain found in reverse transcriptase / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN SPUMARETROVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsRety, S. / Delelis, O. / Rezabkova, L. / Dubanchet, B. / Silhan, J. / Lewit-Bentley, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structural Studies of the Catalytic Core of the Primate Foamy Virus (Pfv-1) Integrase
Authors: Rety, S. / Rezabkova, L. / Dubanchet, B. / Silhan, J. / Legrand, P. / Lewit-Bentley, A.
History
DepositionFeb 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTEGRASE
B: INTEGRASE
C: INTEGRASE
D: INTEGRASE
E: INTEGRASE
F: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,79612
Polymers135,4676
Non-polymers3306
Water5,657314
1
A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2654
Polymers45,1562
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-17.2 kcal/mol
Surface area17050 Å2
MethodPISA
2
E: INTEGRASE
F: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2654
Polymers45,1562
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-20.5 kcal/mol
Surface area16820 Å2
MethodPISA
3
C: INTEGRASE
D: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2654
Polymers45,1562
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-17.6 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)84.767, 89.232, 177.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
INTEGRASE / / IN / P42IN


Mass: 22577.797 Da / Num. of mol.: 6 / Fragment: CATALYTIC CORE, RESIDUES 861-1060 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Strain: HSRV2 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14350
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MET ...ENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 1004 TO MET ENGINEERED RESIDUE IN CHAIN B, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN B, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 1004 TO MET ENGINEERED RESIDUE IN CHAIN C, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN C, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 1004 TO MET ENGINEERED RESIDUE IN CHAIN D, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN D, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 1004 TO MET ENGINEERED RESIDUE IN CHAIN E, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN E, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN E, LEU 1004 TO MET ENGINEERED RESIDUE IN CHAIN F, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN F, ILE 978 TO MET ENGINEERED RESIDUE IN CHAIN F, LEU 1004 TO MET

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.03 % / Description: NONE
Crystal growDetails: 1.8-2M AMMONIUM FORMATE 100MM HEPES, PH 7.5 5MM MNCL2 10-15% GLYCEROL

-
Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2009 / Details: KB-MIRRORS
RadiationMonochromator: SI (111) CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.06→49.23 Å / Num. obs: 78830 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 71

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X74
Resolution: 2.06→44.62 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.607 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27004 3937 5 %RANDOM
Rwork0.22574 ---
obs0.22793 74893 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.994 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---1.73 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.06→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8708 0 6 314 9028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.97212247
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85623.826379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.985151495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9271542
X-RAY DIFFRACTIONr_chiral_restr0.070.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9552.55468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7193.58949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.58943516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4755.53298
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.055→2.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 173 -
Rwork0.286 3718 -
obs--63.12 %

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more