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- PDB-3abe: Structure of human REV7 in complex with a human REV3 fragment in ... -

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Basic information

Entry
Database: PDB / ID: 3abe
TitleStructure of human REV7 in complex with a human REV3 fragment in a tetragonal crystal
Components
  • DNA polymerase zeta catalytic subunit
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsCELL CYCLE/REPLICATION / DNA POLYMERASE / HORMA / DNA REPLICATION / TRANSLESION SYNTHESIS / Cell cycle / Cell division / Mitosis / DNA damage / DNA repair / DNA-binding / DNA-directed DNA polymerase / CELL CYCLE-REPLICATION 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 / 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 ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / 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 / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / 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 / 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-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
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 / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA 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 / 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 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 / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA polymerase zeta catalytic subunit / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHara, K. / Hashimoto, H. / Murakumo, Y. / Kobayashi, S. / Kogame, T. / Unzai, S. / Akashi, S. / Takeda, S. / Shimizu, T. / Sato, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase {zeta} and REV1
Authors: Hara, K. / Hashimoto, H. / Murakumo, Y. / Kobayashi, S. / Kogame, T. / Unzai, S. / Akashi, S. / Takeda, S. / Shimizu, T. / Sato, M.
History
DepositionDec 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Mitotic spindle assembly checkpoint protein MAD2B
Z: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)31,7342
Polymers31,7342
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-17 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.517, 76.517, 118.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-216-

HOH

21C-217-

HOH

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Components

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


Mass: 26101.236 Da / Num. of mol.: 1 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV7 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UI95
#2: Protein DNA polymerase zeta catalytic subunit / REV3 / hREV3


Mass: 5632.319 Da / Num. of mol.: 1 / Fragment: residues 1847-1898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV3 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60673
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 20000, 8% PEG 550 MME, 0.8M sodium formate, 0.1M tris-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11076 / % possible obs: 96.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.1 / % possible all: 81.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ABD

3abd


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.709 / SU ML: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28149 526 4.8 %RANDOM
Rwork0.24046 ---
obs0.24242 10491 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.66 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å20 Å20 Å2
2---5.09 Å20 Å2
3---10.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 14 1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221701
X-RAY DIFFRACTIONr_bond_other_d00.021117
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9742324
X-RAY DIFFRACTIONr_angle_other_deg4.11932738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98725.30366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.346154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021847
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02296
X-RAY DIFFRACTIONr_nbd_refined0.2750.2447
X-RAY DIFFRACTIONr_nbd_other0.2730.21188
X-RAY DIFFRACTIONr_nbtor_refined0.2130.2850
X-RAY DIFFRACTIONr_nbtor_other0.1190.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0430.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5420.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0150.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.51340
X-RAY DIFFRACTIONr_mcbond_other0.1321.5422
X-RAY DIFFRACTIONr_mcangle_it1.09721780
X-RAY DIFFRACTIONr_scbond_it1.593673
X-RAY DIFFRACTIONr_scangle_it2.3174.5544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 30 -
Rwork0.305 629 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.0585 Å / Origin y: 17.0467 Å / Origin z: -16.7999 Å
111213212223313233
T0.0394 Å20.006 Å20.0054 Å2-0.417 Å20.0246 Å2---0.0969 Å2
L10.2981 °20.1436 °20.1587 °2-3.2262 °2-0.51 °2--3.1311 °2
S0.0834 Å °1.0071 Å °0.3473 Å °-0.2167 Å °-0.0383 Å °-0.1053 Å °0.1322 Å °-0.0536 Å °-0.0451 Å °

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