[English] 日本語
Yorodumi
- PDB-4ba9: The structural basis for the coordination of Y-family Translesion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ba9
TitleThe structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
ComponentsDNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
KeywordsTRANSFERASE / TLS / DNA REPAIR
Function / homology
Function and homology information


deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis ...deoxycytidyl transferase activity / nucleotide-excision repair, DNA gap filling / error-free translesion synthesis / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : ...DNA repair protein Rev1, C-terminal domain / DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / BRCA1 C Terminus (BRCT) domain / 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. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DNA polymerase kappa / DNA repair protein REV1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsGrummitt, C.G. / Kilkenny, M.L. / Frey, A. / Roe, S.M. / Oliver, A.W. / Sale, J.E. / Pearl, L.H.
CitationJournal: To be Published
Title: The Structural Basis for the Coordination of Y- Family Translesion DNA Polymerases by Rev1
Authors: Grummitt, C.G. / Kilkenny, M.L. / Frey, A. / Roe, S.M. / Oliver, A.W. / Sale, J.E. / Pearl, L.H.
History
DepositionSep 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,02624
Polymers78,2456
Non-polymers78118
Water2,864159
1
A: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
B: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
C: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
D: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63715
Polymers52,1634
Non-polymers47411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-116.5 kcal/mol
Surface area21940 Å2
MethodPISA
2
E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules

E: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
F: DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77918
Polymers52,1634
Non-polymers61514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6580 Å2
ΔGint-171.1 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.750, 105.750, 424.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1 / DINB PROTEIN / DINPALPHA INTEGRIN-BINDING PROTEIN 80 / AIBP80 / REV1-LIKE TERMINAL DEOXYCYTIDYL ...DINB PROTEIN / DINPALPHA INTEGRIN-BINDING PROTEIN 80 / AIBP80 / REV1-LIKE TERMINAL DEOXYCYTIDYL TRANSFERASE / REV1


Mass: 13040.846 Da / Num. of mol.: 6 / Fragment: C-TERMINAL POLYMERASE INTERACTING DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FUSION OF HUMAN REV-1 C-TERMINAL POLYMERASE INTERACTING DOMAIN (REV1-PID) WITH THE REV-1 INTERACTING MOTIF OF POLYMERASE KAPPA (POLKAPPA-RIM).
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PTWO-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9UBT6, UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.84 % / Description: NONE
Crystal growDetails: 100 MM HEPES.NAOH PH 8.0, 10 MM MGCL2, 5 MM NICL2, 7-9% (W/V) PEG 3350, 4% (V/V) 2,2,2-TRIFLUOROETHANOL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9919
DetectorDate: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.73→84.08 Å / Num. obs: 24571 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 74.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.73→42.82 Å / Cor.coef. Fo:Fc: 0.9222 / Cor.coef. Fo:Fc free: 0.8926 / SU R Cruickshank DPI: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.804 / SU Rfree Blow DPI: 0.316 / SU Rfree Cruickshank DPI: 0.317
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG NI. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5295. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=18.
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1256 5.11 %RANDOM
Rwork0.2144 ---
obs0.2162 24564 98.7 %-
Displacement parametersBiso mean: 67.86 Å2
Baniso -1Baniso -2Baniso -3
1--6.4053 Å20 Å20 Å2
2---6.4053 Å20 Å2
3---12.8107 Å2
Refine analyzeLuzzati coordinate error obs: 0.404 Å
Refinement stepCycle: LAST / Resolution: 2.73→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 18 159 5295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027032HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2542SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it5218HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion3.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion678SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6167SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.85 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3127 158 5.3 %
Rwork0.2465 2823 -
all0.2499 2981 -
obs--98.7 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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