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

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Basic information

Entry
Database: PDB / ID: 3abd
TitleStructure of human REV7 in complex with a human REV3 fragment in a monoclinic crystal
Components
  • DNA polymerase zeta catalytic subunit
  • Mitotic spindle assembly checkpoint protein MAD2B
KeywordsCELL CYCLE/REPLICATION / DNA POLYMERASE / HORMA / DNA REPLICATION / TRANSLESION DNA 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 / telomere maintenance in response to DNA damage / 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 epithelial to mesenchymal transition / negative regulation of transcription by competitive promoter 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 / telomere maintenance in response to DNA damage / 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 epithelial to mesenchymal transition / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of ubiquitin protein ligase activity / negative regulation of double-strand break repair via homologous recombination / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of epithelial to mesenchymal transition / error-prone translesion synthesis / 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 / site of double-strand break / positive regulation of peptidyl-serine phosphorylation / chromosome / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / 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) / DNA polymerase zeta catalytic subunit / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / 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 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 / 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 / MIR / Resolution: 1.9 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
Category: database_2 / 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

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


Theoretical massNumber of molelcules
Total (without water)63,4674
Polymers63,4674
Non-polymers00
Water4,630257
1
A: Mitotic spindle assembly checkpoint protein MAD2B
X: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)31,7342
Polymers31,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area10210 Å2
MethodPISA
2
B: Mitotic spindle assembly checkpoint protein MAD2B
Y: DNA polymerase zeta catalytic subunit


Theoretical massNumber of molelcules
Total (without water)31,7342
Polymers31,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-17 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.870, 50.009, 107.275
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.84 Å3/Da / Density % sol: 33.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 2000 MME, 0.8M sodium formate, 0.1M tris-HCl pH 7.5,, 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: 1.9→50 Å / Num. obs: 35667 / % possible obs: 97.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.7 / % possible all: 83.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
SOLVEphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.618 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24074 1780 5 %RANDOM
Rwork0.18669 ---
obs0.18939 33833 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: 19.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 0 257 3617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223361
X-RAY DIFFRACTIONr_bond_other_d00.023165
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9794577
X-RAY DIFFRACTIONr_angle_other_deg1.11537361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52224.779136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20415583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7381512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213608
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02594
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_it0.9271.52104
X-RAY DIFFRACTIONr_mcbond_other0.251.5822
X-RAY DIFFRACTIONr_mcangle_it1.71623453
X-RAY DIFFRACTIONr_scbond_it2.74231257
X-RAY DIFFRACTIONr_scangle_it4.4454.51124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 88 -
Rwork0.217 2050 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2894-0.09470.56212.01520.32641.6599-0.0021-0.11840.00320.13580.01760.01580.0018-0.1246-0.01550.0542-0.0001-0.00450.0701-0.02140.010512.3730.1110.444
20.9878-0.0363-0.01172.12640.55761.73290.07550.0512-0.0225-0.2108-0.0372-0.012-0.0057-0.0142-0.03830.08610.01840.0080.0581-0.02440.015227.00522.70941.389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 211
2X-RAY DIFFRACTION2B10 - 211

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