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- PDB-5wmb: Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex ... -

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Basic information

Entry
Database: PDB / ID: 5wmb
TitleStructure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)
Components
  • DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3')
  • DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
  • DNA repair protein REV1
Keywordstransferase/dna / benzo[a]pyrene Rev1 polymerase carcinogen lesion bypass / DNA BINDING PROTEIN / transferase-dna complex
Function / homology
Function and homology information


deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / chromatin / mitochondrion / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1490 / DNA repair protein Rev1 / BRCT domain, a BRCA1 C-terminus domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1490 / DNA repair protein Rev1 / BRCT domain, a BRCA1 C-terminus domain / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / Helix non-globular / Special / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA repair protein REV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRechkoblit, O. / Kolbanovsky, A. / Landes, H. / Geacintov, N.E. / Aggarwal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 CA200575 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES024050 United States
CitationJournal: Nat Commun / Year: 2017
Title: Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase.
Authors: Rechkoblit, O. / Kolbanovskiy, A. / Landes, H. / Geacintov, N.E. / Aggarwal, A.K.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...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 / struct_conn / struct_conn_type
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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3')
T: DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')
A: DNA repair protein REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76220
Polymers58,2893
Non-polymers1,47317
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-52 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.307, 65.476, 131.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3')


Mass: 3798.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3')


Mass: 5037.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#3: Protein DNA repair protein REV1 / / Reversionless protein 1


Mass: 49452.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus
References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 6 types, 178 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.25 M sodium citrate pH 6.0 buffer 15-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→65.83 Å / Num. obs: 26824 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 18.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQ4

2aq4


Resolution: 2.25→65.83 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.251 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1345 5 %RANDOM
Rwork0.1699 ---
obs0.17223 25424 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--1.91 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.25→65.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 552 91 161 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0184290
X-RAY DIFFRACTIONr_bond_other_d0.0020.023725
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.8655890
X-RAY DIFFRACTIONr_angle_other_deg1.01138685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03624.051158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22315652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7091522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
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_it2.263.4781759
X-RAY DIFFRACTIONr_mcbond_other2.2573.4751758
X-RAY DIFFRACTIONr_mcangle_it3.5335.2012206
X-RAY DIFFRACTIONr_mcangle_other3.5345.2032207
X-RAY DIFFRACTIONr_scbond_it3.2954.3422531
X-RAY DIFFRACTIONr_scbond_other3.284.3422531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2436.4113681
X-RAY DIFFRACTIONr_long_range_B_refined7.42142.3474857
X-RAY DIFFRACTIONr_long_range_B_other7.40442.2094825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.247→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 91 -
Rwork0.249 1802 -
obs--97.83 %

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