[English] 日本語
Yorodumi
- PDB-4fjo: Structure of the Rev1 CTD-Rev3/7-Pol kappa RIR complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fjo
TitleStructure of the Rev1 CTD-Rev3/7-Pol kappa RIR complex
Components
  • (DNA polymerase ...) x 2
  • DNA repair protein REV1
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsTRANSFERASE/DNA BINDING PROTEIN / Translesion Synthesis / TRANSFERASE -DNA BINDING PROTEIN complex / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


: / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / Termination of translesion DNA synthesis / Dual Incision in GG-NER ...: / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / HDR through Homologous Recombination (HRR) / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / deoxycytidyl transferase activity / telomere maintenance in response to DNA damage / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of epithelial to mesenchymal transition / JUN kinase binding / nucleotide-excision repair, DNA gap filling / negative regulation of ubiquitin protein ligase activity / error-free translesion synthesis / positive regulation of double-strand break repair via nonhomologous end joining / site of DNA damage / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / response to UV / actin filament organization / regulation of cell growth / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / spindle / cellular response to UV / double-strand break repair / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / molecular adaptor activity / DNA-directed DNA polymerase activity / nuclear body / cell cycle / cell division / nucleotide binding / DNA repair / DNA damage response / chromatin / positive regulation of gene expression / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
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 / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / DNA polymerase zeta catalytic subunit ...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 / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / DNA polymerase zeta catalytic subunit / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / Rad18-like CCHC zinc finger / DNA repair protein Rev1 / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase IV / DNApol eta/Rev1, HhH motif / DNA polymerase family B, thumb domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA polymerase zeta catalytic subunit / DNA repair protein REV1 / Mitotic spindle assembly checkpoint protein MAD2B / DNA polymerase kappa
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.718 Å
AuthorsWojtaszek, J. / Lee, C.-J. / Zhou, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric Pol zeta and Pol kappa
Authors: Wojtaszek, J. / Lee, C.J. / D'Souza, S. / Minesinger, B. / Kim, H. / D'Andrea, A.D. / Walker, G.C. / Zhou, P.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 repair protein REV1
B: DNA polymerase kappa
C: Mitotic spindle assembly checkpoint protein MAD2B
D: DNA polymerase zeta catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90413
Polymers40,0524
Non-polymers8529
Water2,360131
1
A: DNA repair protein REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2592
Polymers11,1671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase kappa


Theoretical massNumber of molelcules
Total (without water)1,3031
Polymers1,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitotic spindle assembly checkpoint protein MAD2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0229
Polymers24,2621
Non-polymers7608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)3,3201
Polymers3,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.727, 145.727, 70.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 2 types, 2 molecules AC

#1: Protein DNA repair protein REV1 / / Rev1-like terminal deoxycytidyl transferase


Mass: 11166.859 Da / Num. of mol.: 1 / Fragment: Rev1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rev1, Rev1l / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q920Q2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Protein Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2


Mass: 24262.283 Da / Num. of mol.: 1 / Fragment: REV7 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mad2l2, Mad2b, Rev7 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9D752

-
DNA polymerase ... , 2 types, 2 molecules BD

#2: Protein/peptide DNA polymerase kappa / POLK / DINB protein / DINP


Mass: 1303.467 Da / Num. of mol.: 1 / Fragment: Rev1-interacting Region (RIR) of Pol Kappa
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polk, Dinb1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QUG2
#4: Protein/peptide DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / REV3-like / Seizure-related protein 4


Mass: 3319.850 Da / Num. of mol.: 1 / Fragment: REV7-interacting region of Rev3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rev3l, Polz, Sez4 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61493, DNA-directed DNA polymerase

-
Non-polymers , 3 types, 140 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH8.5, 1.5 M Ammonium dihydrogen phosphate., VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 20970 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.081 / Χ2: 1.295 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.759.30.62510130.8861100
2.75-2.89.50.58210480.9451100
2.8-2.859.40.44810110.9731100
2.85-2.919.60.39610380.9511100
2.91-2.979.50.3210271.051100
2.97-3.049.60.27310441.1211100
3.04-3.129.60.22910121.1241100
3.12-3.29.60.21110431.2321100
3.2-3.39.60.15510421.3231100
3.3-3.49.70.13710311.404199.9
3.4-3.529.60.1210441.4171100
3.52-3.669.70.10810411.6021100
3.66-3.839.70.09810411.51100
3.83-4.039.70.09410561.8411100
4.03-4.299.60.08810451.7731100
4.29-4.629.70.08510641.931100
4.62-5.089.60.07510581.6261100
5.08-5.819.50.05810831.1911100
5.81-7.329.30.04210990.9381100
7.32-508.80.02711300.973195.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å23.97 Å
Translation2.72 Å23.97 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.718→23.975 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.834 / SU ML: 0.28 / σ(F): 1.35 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 1076 5.14 %
Rwork0.2005 --
obs0.2023 20916 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.9 Å2 / Biso mean: 56.2735 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: LAST / Resolution: 2.718→23.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 46 131 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072911
X-RAY DIFFRACTIONf_angle_d0.953954
X-RAY DIFFRACTIONf_chiral_restr0.068464
X-RAY DIFFRACTIONf_plane_restr0.003493
X-RAY DIFFRACTIONf_dihedral_angle_d14.4281093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.718-2.84140.2551470.25072328247596
2.8414-2.99090.33091410.235424382579100
2.9909-3.17790.29291440.230824402584100
3.1779-3.42260.24021200.208724632583100
3.4226-3.76590.25671260.202724922618100
3.7659-4.3080.20341420.17624752617100
4.308-5.41730.19441380.174625312669100
5.4173-23.97560.24641180.21126732791100
Refinement TLS params.Method: refined / Origin x: -38.868 Å / Origin y: 13.8723 Å / Origin z: -9.7001 Å
111213212223313233
T0.1906 Å2-0.0518 Å2-0.1365 Å2-0.0332 Å20.0635 Å2--0.0843 Å2
L2.8907 °20.9869 °2-0.4021 °2-1.692 °20.1719 °2--1.3828 °2
S-0.0347 Å °-0.1798 Å °-0.2219 Å °-0.0147 Å °-0.0343 Å °-0.019 Å °0.0137 Å °0.0415 Å °-0.2808 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1153 - 1249
2X-RAY DIFFRACTION1allB565 - 574
3X-RAY DIFFRACTION1allC1 - 210
4X-RAY DIFFRACTION1allD1865 - 1894
5X-RAY DIFFRACTION1allC1 - 308
6X-RAY DIFFRACTION1allA1 - 1301
7X-RAY DIFFRACTION1allC1 - 479

+
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