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- PDB-6m7a: Structure of REV7-R124A complexed with SHLD3(28-73) -

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Basic information

Entry
Database: PDB / ID: 6m7a
TitleStructure of REV7-R124A complexed with SHLD3(28-73)
Components
  • Mitotic spindle assembly checkpoint protein MAD2B
  • Shieldin complex subunit 3
KeywordsREPLICATION / REV7 / shieldin / SHLD3 / DNA damage
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 / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / cell division / DNA repair / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Shieldin complex subunit 3 / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily
Similarity search - Domain/homology
Shieldin complex subunit 3 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMa, Y.Z. / Li, Y. / Wu, B.X. / Huang, H.D.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004500 China
National Natural Science Foundation of China (NSFC)the Thousand Young Talents Program China
CitationJournal: To Be Published
Title: Structure of REV7-R124A complexed with SHLD3(28-73)
Authors: Ma, Y.Z. / Li, Y. / Wu, B.X. / Huang, H.D.
History
DepositionMar 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD2B
D: Shieldin complex subunit 3
B: Mitotic spindle assembly checkpoint protein MAD2B
C: Shieldin complex subunit 3


Theoretical massNumber of molelcules
Total (without water)59,3254
Polymers59,3254
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-69 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.521, 62.124, 130.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 24281.350 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI95
#2: Protein/peptide Shieldin complex subunit 3 / REV7-interacting novel NHEJ regulator 1 / Shield complex subunit 3


Mass: 5381.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHLD3, FLJ26957, RINN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZNX1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.93 Å3/Da / Density % sol: 36.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaCl Sodium Chloride; 0.1 M Na/K phosphate 6.2; 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 37019 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.433 / Net I/σ(I): 2.4
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 3640 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VU7

3vu7


Resolution: 1.9→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2324 1768 -
Rwork0.1803 --
obs-34077 91.69 %
Displacement parametersBiso mean: 27.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 0 381 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863921
X-RAY DIFFRACTIONf_angle_d1.01945337
X-RAY DIFFRACTIONf_chiral_restr0.0635622
X-RAY DIFFRACTIONf_plane_restr0.0061679
X-RAY DIFFRACTIONf_dihedral_angle_d22.22062411
LS refinement shellResolution: 1.8969→1.9482 Å
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.2207 --
obs-1053 39 %

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