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- PDB-6kto: Crystal structure of human SHLD3-C-REV7-O-REV7-SHLD2 complex -

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Basic information

Entry
Database: PDB / ID: 6kto
TitleCrystal structure of human SHLD3-C-REV7-O-REV7-SHLD2 complex
Components
  • Mitotic spindle assembly checkpoint protein MAD2B
  • Shieldin complex subunit 2
  • Shieldin complex subunit 3
KeywordsREPLICATION / Shieldin / Complex / Conformational dimer / NHEJ
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / zeta DNA polymerase complex / positive regulation of isotype switching / 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 / regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via nonhomologous end joining ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / zeta DNA polymerase complex / positive regulation of isotype switching / 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 / regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / negative regulation of ubiquitin protein ligase activity / telomere maintenance in response to DNA damage / positive regulation of peptidyl-serine phosphorylation / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / actin filament organization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / spindle / transcription corepressor activity / double-strand break repair / actin cytoskeleton / site of double-strand break / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / cell division / DNA repair / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Shieldin complex subunit 2 / Protein FAM35A, C-terminal domain / : / : / Shieldin complex subunit 2, C-terminal / Shieldin complex subunit 2, first OB fold domain / Shieldin complex subunit 2, second OB fold domain / Shieldin complex subunit 3 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain ...Shieldin complex subunit 2 / Protein FAM35A, C-terminal domain / : / : / Shieldin complex subunit 2, C-terminal / Shieldin complex subunit 2, first OB fold domain / Shieldin complex subunit 2, second OB fold domain / Shieldin complex subunit 3 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Shieldin complex subunit 3 / Shieldin complex subunit 2 / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44976331487 Å
AuthorsLiang, L. / Yin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis for assembly of the shieldin complex and its implications for NHEJ.
Authors: Liang, L. / Feng, J. / Zuo, P. / Yang, J. / Lu, Y. / Yin, Y.
History
DepositionAug 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Mitotic spindle assembly checkpoint protein MAD2B
B: Mitotic spindle assembly checkpoint protein MAD2B
C: Shieldin complex subunit 3
D: Shieldin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)65,7314
Polymers65,7314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-56 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.843, 93.843, 325.377
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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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: 26187.352 Da / Num. of mol.: 2
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 Shieldin complex subunit 3 / REV7-interacting novel NHEJ regulator 1 / Shield complex subunit 3


Mass: 7402.546 Da / Num. of mol.: 1
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: Protein Shieldin complex subunit 2 / Protein FAM35A / RINN1-REV7-interacting novel NHEJ regulator 2 / Shield complex subunit 2


Mass: 5953.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHLD2, FAM35A, RINN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86V20

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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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M Magnesium chloride hexahydrate, 0.1M HEPES 7.5, 22% w/v Poly (acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.44→50 Å / Num. obs: 11237 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 58.7354852027 Å2 / Rpim(I) all: 0.058 / Net I/σ(I): 12.75
Reflection shellResolution: 3.45→3.72 Å / Num. unique obs: 2312 / Rpim(I) all: 0.452

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vu7

3vu7


Resolution: 3.44976331487→46.4411009446 Å / SU ML: 0.408163546905 / Cross valid method: FREE R-VALUE / σ(F): 1.36702633773 / Phase error: 24.9565654608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.268599868523 591 5.25941087479 %
Rwork0.241566498418 10646 -
obs0.242976454103 11237 93.8920454545 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.6481043069 Å2
Refinement stepCycle: LAST / Resolution: 3.44976331487→46.4411009446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 0 0 3710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01301239053643799
X-RAY DIFFRACTIONf_angle_d1.49381054265163
X-RAY DIFFRACTIONf_chiral_restr0.370498071853603
X-RAY DIFFRACTIONf_plane_restr0.00881563399627650
X-RAY DIFFRACTIONf_dihedral_angle_d23.91070703191439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4498-3.79680.3431399535761080.287091349792042X-RAY DIFFRACTION74.6268656716
3.7968-4.34580.2942989720761670.2373151908982750X-RAY DIFFRACTION100
4.3458-5.47390.2007026004361500.2162796903082827X-RAY DIFFRACTION100
5.4739-46.440.2811776569661660.2471645291893027X-RAY DIFFRACTION100

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