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- PDB-4ztj: Crystal Structure of the Prototype Foamy Virus Intasome with a 2-... -

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Basic information

Entry
Database: PDB / ID: 4ztj
TitleCrystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
  • PFV INTEGRASE
Keywordstransferase/DNA/inhibitor / TRANSFERASE-DNA COMPLEX / DNA INTEGRATION / VIRAL PROTEIN / RECOMBINATION-INHIBITOR-DNA COMPLEX / transferase-DNA-inhibitor complex
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 / host cell ...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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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
Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / 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 / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #110 / Endonuclease III; domain 1 - #70 / 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 / Arc Repressor Mutant, subunit A / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Endonuclease III; domain 1 / SH3 type barrels. - #140 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / RNase H / Integrase core domain / SH3 type barrels. / 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 / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4RT / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.67 Å
AuthorsKlein, D.J. / Patel, S.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors.
Authors: Raheem, I.T. / Walji, A.M. / Klein, D. / Sanders, J.M. / Powell, D.A. / Abeywickrema, P. / Barbe, G. / Bennet, A. / Clas, S.D. / Dubost, D. / Embrey, M. / Grobler, J. / Hafey, M.J. / ...Authors: Raheem, I.T. / Walji, A.M. / Klein, D. / Sanders, J.M. / Powell, D.A. / Abeywickrema, P. / Barbe, G. / Bennet, A. / Clas, S.D. / Dubost, D. / Embrey, M. / Grobler, J. / Hafey, M.J. / Hartingh, T.J. / Hazuda, D.J. / Miller, M.D. / Moore, K.P. / Pajkovic, N. / Patel, S. / Rada, V. / Rearden, P. / Schreier, J.D. / Sisko, J. / Steele, T.G. / Truchon, J.F. / Wai, J. / Xu, M. / Coleman, P.J.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PFV INTEGRASE
B: PFV INTEGRASE
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,22616
Polymers99,9444
Non-polymers1,28312
Water3,297183
1
A: PFV INTEGRASE
B: PFV INTEGRASE
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules

A: PFV INTEGRASE
B: PFV INTEGRASE
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,45332
Polymers199,8878
Non-polymers2,56624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area28280 Å2
ΔGint-288 kcal/mol
Surface area56320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.960, 158.960, 124.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PFV INTEGRASE / Pr125Pol


Mass: 44456.695 Da / Num. of mol.: 2 / Fragment: unp residues 752-1143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: P14350

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')


Mass: 5834.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SYNTHETIC / Source: (gene. exp.) Human spumaretrovirus / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')


Mass: 5195.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Production host: synthetic construct (others)

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Non-polymers , 6 types, 195 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-4RT / (1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione


Mass: 487.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23ClFN3O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.25 M AMMONIUM SULFATE, 25% (V/V) GLYCEROL, 4.8% (V/V) 1,6-HEXANEDIOL, 50 MM MES-NAOH, 1MM EDTA, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→49.001 Å / Num. obs: 45839 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 86.34 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.7 / Num. measured all: 610998
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all
2.67-2.679130.9725883452
12.328-49.00111.10.0636061548

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.67→46.83 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.9213 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 2306 5.04 %RANDOM
Rwork0.1956 ---
obs0.1969 45774 99.97 %-
Displacement parametersBiso max: 180.49 Å2 / Biso mean: 71.88 Å2 / Biso min: 40.32 Å2
Baniso -1Baniso -2Baniso -3
1--6.735 Å20 Å20 Å2
2---6.735 Å20 Å2
3---13.4699 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: final / Resolution: 2.67→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 732 77 183 5324
Biso mean--80.79 63.77 -
Num. residues----588
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1673SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC8
X-RAY DIFFRACTIONt_gen_planes702HARMONIC8
X-RAY DIFFRACTIONt_it5343HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion705SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6013SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5343HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7453HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion21.06
LS refinement shellResolution: 2.67→2.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 179 5.39 %
Rwork0.2396 3145 -
all0.2435 3324 -
obs--99.97 %

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