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- PDB-2x6n: Human foamy virus integrase - catalytic core. Manganese-bound str... -

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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


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / virion component / viral penetration into host nucleus / 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 / establishment of integrated proviral latency / RNA-directed DNA polymerase / virion component / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase ...Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / 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
: / 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
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_dist_value / _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_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
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
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

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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


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

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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: 2.64 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

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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

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X74

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 %

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