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- PDB-4ext: Structure of polymerase-interacting domain of human Rev1 in compl... -

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Basic information

Entry
Database: PDB / ID: 4ext
TitleStructure of polymerase-interacting domain of human Rev1 in complex with translesional synthesis polymerase zeta
Components
  • DNA repair protein REV1
  • Mitotic spindle assembly checkpoint protein MAD2B
  • peptide from DNA polymerase zeta catalytic subunit
KeywordsTRANSFERASE/TRANSCRIPTION / Rev1 / Rev3 / Rev7 / polymerase-interacting domain / Y-family polymerase / B-family polymerase / Translesional synthesis polymerase / DNA damage tolerance / Scaffold / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / JUN kinase binding / negative regulation of cell-cell adhesion mediated by cadherin ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / deoxycytidyl transferase activity / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / JUN kinase binding / negative regulation of cell-cell adhesion mediated by cadherin / 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 / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / positive regulation of epithelial to mesenchymal transition / response to UV / positive regulation of peptidyl-serine phosphorylation / Translesion synthesis by REV1 / Translesion synthesis by POLK / actin filament organization / Translesion synthesis by POLI / negative regulation of DNA-binding transcription factor activity / 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 / spindle / DNA-templated DNA replication / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-strand break repair / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / cell division / nucleotide binding / 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 / 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 family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / 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, Y-family, little finger domain / DNA polymerase, palm domain superfamily / impB/mucB/samB family C-terminal domain / 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 repair protein REV1 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLiu, D.N. / Ryu, K.S. / Ko, J.S. / Choi, B.S.
CitationJournal: To be Published
Title: Insights into the scaffold mechanism of human Rev1 in translesional synthesis revealed by structural studies on its polymerase-interacting domain
Authors: Liu, D.N. / Ryu, K.S. / Ko, J.S. / Choi, B.S.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DNA repair protein REV1
B: peptide from DNA polymerase zeta catalytic subunit
C: Mitotic spindle assembly checkpoint protein MAD2B


Theoretical massNumber of molelcules
Total (without water)37,3273
Polymers37,3273
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-21 kcal/mol
Surface area16120 Å2
MethodPISA
2
A: DNA repair protein REV1

B: peptide from DNA polymerase zeta catalytic subunit
C: Mitotic spindle assembly checkpoint protein MAD2B


Theoretical massNumber of molelcules
Total (without water)37,3273
Polymers37,3273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_545-x,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.699, 71.523, 84.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA repair protein REV1 / Rev1 / hRev1 / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 11122.806 Da / Num. of mol.: 1
Fragment: Protein interaction domain, UNP residues 1156-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein/peptide peptide from DNA polymerase zeta catalytic subunit / Protein reversionless 3-like / REV3-like / hREV3


Mass: 2585.115 Da / Num. of mol.: 1 / Fragment: UNP residues 1873-1895
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Plasmid: pDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60673
#3: Protein Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2 / REV7 homolog / hREV7


Mass: 23619.578 Da / Num. of mol.: 1 / Fragment: Regulartory subunit, UNP residues 7-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Plasmid: pDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UI95
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.96 Å3/Da / Density % sol: 37.27 % / Mosaicity: 0.75 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1M HEPES-Na (pH 7.5), 0.1M NH4-citrate tribasic (pH 7.0), 19-21% PEG 3350, EVAPORATION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 23435 / Num. obs: 22498 / % possible obs: 96 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.042 / Χ2: 1.4 / Net I/σ(I): 28.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.40.29718620.722180.9
1.97-2.053.40.26821180.809192.7
2.05-2.144.30.22122200.914196.2
2.14-2.254.70.17522331.042196.7
2.25-2.395.20.13722961.238197.8
2.39-2.585.60.09922621.254198.6
2.58-2.846.10.06723151.368198.6
2.84-3.256.50.04523441.632199.4
3.25-4.096.80.03123571.774199.5
4.09-506.40.02724911.891198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 2232 9.4 %Random
Rwork0.2235 ---
obs-22482 94.4 %-
Solvent computationBsol: 59.1968 Å2
Displacement parametersBiso max: 88.3 Å2 / Biso mean: 40.0922 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1-7.013 Å20 Å20 Å2
2---5.578 Å20 Å2
3----1.435 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 115 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.171
X-RAY DIFFRACTIONc_mcbond_it1.7081.5
X-RAY DIFFRACTIONc_scbond_it2.3972
X-RAY DIFFRACTIONc_mcangle_it2.8222
X-RAY DIFFRACTIONc_scangle_it3.6662.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.41351550.35631386154165.8
1.97-2.050.34242370.31841909214691.2
2.05-2.140.2982210.25982006222796.3
2.14-2.250.2922160.23852074229097.1
2.25-2.390.29192560.23192041229797.7
2.39-2.580.2592370.22572096233398.5
2.58-2.840.30992160.2472117233398.6
2.84-3.250.30542470.23572157240499.5
3.25-4.090.23172220.18492169239199.7
4.09-500.28422250.20472295252099.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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