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- PDB-3dlr: Crystal structure of the catalytic core domain from PFV integrase -

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Basic information

Entry
Database: PDB / ID: 3dlr
TitleCrystal structure of the catalytic core domain from PFV integrase
ComponentsIntegrase
KeywordsTRANSFERASE / Retroviral integrase / RVE superfamily domain / DNA integration / DNA recombination / Endonuclease / Hydrolase / Magnesium / Metal-binding / Multifunctional enzyme / Nuclease / Nucleotidyltransferase / Nucleus / Virion
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / 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 / Ribonuclease H-like superfamily/Ribonuclease H ...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. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsValkov, E. / Cherepanov, P.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Functional and structural characterization of the integrase from the prototype foamy virus.
Authors: Valkov, E. / Gupta, S.S. / Hare, S. / Helander, A. / Roversi, P. / McClure, M. / Cherepanov, P.
History
DepositionJun 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms ...entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software / struct / struct_conn
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.name / _software.version / _struct.pdbx_descriptor / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)22,6712
Polymers22,6471
Non-polymers241
Water86548
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3424
Polymers45,2932
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2180 Å2
ΔGint-24 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.140, 52.140, 239.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe second part of the biologically-relevant dimer is generated by the two-fold operation: x, 1-x+y, 1/6-z

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Components

#1: Protein Integrase / / Integrase / IN / p42In


Mass: 22646.635 Da / Num. of mol.: 1 / Fragment: catalytic core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: pol / Plasmid: pCPH6P-HSRV2(88-286) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P14350
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.79 %
Description: 1cxu was used as a search model for molecular replacement. Solution found in PHASER (Euler angles 310.7, 84.0, 41.7; fractional coordinates -1.272, 0.422, 0.077) was used as a starting ...Description: 1cxu was used as a search model for molecular replacement. Solution found in PHASER (Euler angles 310.7, 84.0, 41.7; fractional coordinates -1.272, 0.422, 0.077) was used as a starting model for density modification in SOLOMON to improve and extend Se-SAD derived phases.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 M ammonium formate, 0.2 M magnesium cloride, 5 mM dithiotreitol, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.95373
SYNCHROTRONESRF BM1420.97837
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJan 26, 2008
MARMOSAIC 225 mm CCD2CCDJan 26, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) monochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.953731
20.978371
ReflectionResolution: 2.2→45.18 Å / Num. all: 10584 / Num. obs: 10584 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.105 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1477 / Rsym value: 0.681 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1cxu
Resolution: 2.2→45.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.771 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25922 1042 9.8 %RANDOM
Rwork0.20905 ---
obs0.21394 9540 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 1 48 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.010.0221255
X-RAY DIFFRACTIONf_bond_other_d
X-RAY DIFFRACTIONf_angle_refined_deg1.1221.9691712
X-RAY DIFFRACTIONf_angle_other_deg
X-RAY DIFFRACTIONf_dihedral_angle_1_deg5.8385152
X-RAY DIFFRACTIONf_dihedral_angle_2_deg35.37123.11145
X-RAY DIFFRACTIONf_dihedral_angle_3_deg16.04115202
X-RAY DIFFRACTIONf_dihedral_angle_4_deg16.931154
X-RAY DIFFRACTIONf_chiral_restr0.0730.2201
X-RAY DIFFRACTIONf_gen_planes_refined0.0040.02918
X-RAY DIFFRACTIONf_gen_planes_other
X-RAY DIFFRACTIONf_nbd_refined0.1970.2523
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined0.3070.2860
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined0.1140.260
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined0.1490.239
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined0.1310.24
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it0.5581.5791
X-RAY DIFFRACTIONf_mcbond_other
X-RAY DIFFRACTIONf_mcangle_it1.02521264
X-RAY DIFFRACTIONf_scbond_it1.7463535
X-RAY DIFFRACTIONf_scangle_it2.4724.5448
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 75 -
Rwork0.219 683 -
obs--98.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.0876-0.174-0.13661.78-0.77422.68470.00580.074-0.16-0.04050.0673-0.04450.25530.0082-0.0731-0.05930.0565-0.0181-0.1625-0.0245-0.1432-0.06619.71514.154
229.940913.184611.665633.5029-8.820217.701-0.43371.74110.824-0.4456-0.18780.5624-0.26351.15410.62160.013-0.1786-0.07270.24070.0904-0.1504-9.2122.506-3.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA119 - 27114 - 166
2X-RAY DIFFRACTION2AA293 - 304188 - 199

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