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- PDB-4gk0: Crystal structure of human Rev3-Rev7-Rev1 complex -

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Basic information

Entry
Database: PDB / ID: 4gk0
TitleCrystal structure of human Rev3-Rev7-Rev1 complex
Components
  • 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 / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase 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 / JUN kinase binding ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase 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 / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / error-free translesion synthesis / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / telomere maintenance in response to 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / chromosome / 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 / DNA-directed DNA polymerase activity / cell division / nucleotide binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / 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 / 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. / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / HORMA domain superfamily / : / DNA polymerase-iota, thumb domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / 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, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / 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
DNA polymerase zeta catalytic subunit / DNA repair protein REV1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)95,5436
Polymers95,5436
Non-polymers00
Water00
1
E: DNA repair protein REV1

A: Mitotic spindle assembly checkpoint protein MAD2B
C: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)47,7723
Polymers47,7723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_455-x-1/2,y+1/2,-z1
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29 kcal/mol
Surface area14990 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)121.089, 71.887, 106.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 1847-1898
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

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium citrate, 1.95M sodium formate, 20mM DTT , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 23773 / Num. obs: 23773 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2511 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABD

3abd


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.457 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27338 1267 5.1 %RANDOM
Rwork0.21806 ---
all0.22094 23773 --
obs0.22094 23773 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.344 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0 Å20 Å2
2---1.65 Å2-0 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 0 0 4987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195080
X-RAY DIFFRACTIONr_bond_other_d00.025050
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9746893
X-RAY DIFFRACTIONr_angle_other_deg3.494311645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.255608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.825.398226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.74215951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1511520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215526
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021054
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 88 -
Rwork0.286 1738 -
obs--96.82 %

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