[English] 日本語
Yorodumi
- PDB-4gk5: Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gk5
TitleCrystal structure of human Rev3-Rev7-Rev1-Polkappa complex
Components
  • DNA polymerase kappa
  • DNA polymerase zeta catalytic subunit
  • DNA repair protein REV1
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsTRANSFERASE / translesion polymerases complex / four-helix bundle / beta-hairpin domain / anti-parallel sheets / translesion DNA synthesis / polymerase switch / none
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / nucleotide-excision repair, DNA gap filling / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / nucleotide-excision repair, DNA gap filling / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / error-free translesion synthesis / negative regulation of ubiquitin protein ligase activity / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / telomere maintenance in response to DNA damage / positive regulation of peptidyl-serine phosphorylation / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / response to UV / actin filament organization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / regulation of cell growth / Termination of translesion DNA synthesis / negative regulation of canonical Wnt signaling pathway / double-strand break repair via homologous recombination / negative regulation of protein catabolic process / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / cellular response to UV / transcription corepressor activity / double-strand break repair / chromosome / site of double-strand break / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase activity / DNA replication / nuclear body / cell division / DNA repair / nucleotide binding / DNA damage response / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion 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) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal ...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) / DNA polymerase zeta catalytic subunit / : / DNA polymerase zeta catalytic subunit, N-terminal / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / DNA repair protein Rev1 / C4-type zinc-finger of DNA polymerase delta / : / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta catalytic subunit-like, N-terminal domain / Rad18-like CCHC zinc finger / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / 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 / : / DNA polymerase family B, thumb domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / BRCA1 C Terminus (BRCT) domain / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / 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
DNA polymerase zeta catalytic subunit / DNA polymerase kappa / DNA repair protein REV1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsTao, J. / Min, X. / Wei, X.
CitationJournal: Protein Cell / Year: 2012
Title: Structural insights into the assembly of human translesion polymerase complexes
Authors: Xie, W. / Yang, X. / Xu, M. / Jiang, T.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD2B
B: Mitotic spindle assembly checkpoint protein MAD2B
C: DNA polymerase zeta catalytic subunit
D: DNA polymerase zeta catalytic subunit
E: DNA repair protein REV1
F: DNA repair protein REV1
G: DNA polymerase kappa


Theoretical massNumber of molelcules
Total (without water)96,8197
Polymers96,8197
Non-polymers00
Water00
1
A: Mitotic spindle assembly checkpoint protein MAD2B
C: DNA polymerase zeta catalytic subunit

E: DNA repair protein REV1
G: DNA polymerase kappa


Theoretical massNumber of molelcules
Total (without water)49,0474
Polymers49,0474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1/2,y+1/2,-z1
Buried area4750 Å2
ΔGint-36 kcal/mol
Surface area15060 Å2
MethodPISA
2
F: DNA repair protein REV1

B: Mitotic spindle assembly checkpoint protein MAD2B
D: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)47,7723
Polymers47,7723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_456-x-1/2,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-29 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.998, 72.762, 104.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2 / REV7 homolog / hREV7


Mass: 26960.033 Da / Num. of mol.: 2 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UI95
#2: Protein DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / REV3-like / hREV3


Mass: 5632.319 Da / Num. of mol.: 2 / Fragment: Rev7-binding domain, UNP residues 1874-1893
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60673, DNA-directed DNA polymerase
#3: Protein DNA repair protein REV1 / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 15179.386 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 1117-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#4: Protein/peptide DNA polymerase kappa / DINB protein / DINP


Mass: 1275.519 Da / Num. of mol.: 1 / Fragment: Polkappa RIR peptide, UNP residues 564-573 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 289 K
Method: soaking the rev3-rev7-rev1 crystals with the rir peptide of polkappa
pH: 5.8
Details: 0.1M sodium citrate, 1.95M sodium formate, 20mM DTT , pH 5.8, soaking the Rev3-Rev7-Rev1 crystals with the RIR peptide of Polkappa, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 14623 / Num. obs: 14623 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1531 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GK0

4gk0


Resolution: 3.21→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 770 5 %RANDOM
Rwork0.23154 ---
all0.23408 14623 --
obs0.23408 14623 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.377 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å2-0 Å2
2---2.05 Å20 Å2
3---5.57 Å2
Refinement stepCycle: LAST / Resolution: 3.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 0 0 5058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195152
X-RAY DIFFRACTIONr_bond_other_d00.025121
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9736985
X-RAY DIFFRACTIONr_angle_other_deg3.487311809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5525.304230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.08615967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215598
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021075
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.21→3.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 57 -
Rwork0.335 997 -
obs--95.38 %

+
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