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- PDB-7bgf: CRYSTAL STRUCTURE OF THE N-TERMINAL DIMERIC COILED COIL OF THE HU... -

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Basic information

Entry
Database: PDB / ID: 7bgf
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL DIMERIC COILED COIL OF THE HUMAN CTIP PROTEIN
ComponentsDNA endonuclease RBBP8,CtIP/RBBP8
KeywordsDNA BINDING PROTEIN / COILED COIL / DIMER / DNA REPAIR / HOMOLOGOUS RECOMBINATION
Function / homology
Function and homology information


DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / single-stranded DNA endodeoxyribonuclease activity / blastocyst hatching / DNA strand resection involved in replication fork processing / homologous recombination / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / Homologous DNA Pairing and Strand Exchange ...DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / single-stranded DNA endodeoxyribonuclease activity / blastocyst hatching / DNA strand resection involved in replication fork processing / homologous recombination / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / transcription repressor complex / meiotic cell cycle / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Meiotic recombination / G1/S transition of mitotic cell cycle / transcription corepressor activity / site of double-strand break / Processing of DNA double-strand break ends / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / Hydrolases; Acting on ester bonds / cell division / intracellular membrane-bounded organelle / DNA repair / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
DNA endonuclease Ctp1, N-terminal / DNA endonuclease RBBP8-like / Tumour-suppressor protein CtIP N-terminal domain / DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus
Similarity search - Domain/homology
DNA endonuclease RBBP8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsMorton, C.R. / Pellegrini, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Open Biology / Year: 2021
Title: Structural basis for the coiled-coil architecture of human CtIP.
Authors: Morton, C.R. / Rzechorzek, N.J. / Maman, J.D. / Kuramochi, M. / Sekiguchi, H. / Rambo, R. / Sasaki, Y.C. / Davies, O.R. / Pellegrini, L.
History
DepositionJan 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: DNA endonuclease RBBP8,CtIP/RBBP8
B: DNA endonuclease RBBP8,CtIP/RBBP8


Theoretical massNumber of molelcules
Total (without water)30,5472
Polymers30,5472
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-49 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.598, 86.598, 42.601
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein DNA endonuclease RBBP8,CtIP/RBBP8 / CtBP-interacting protein / CtIP / Retinoblastoma-binding protein 8 / RBBP-8 / Retinoblastoma- ...CtBP-interacting protein / CtIP / Retinoblastoma-binding protein 8 / RBBP-8 / Retinoblastoma-interacting protein and myosin-like / RIM / Sporulation in the absence of SPO11 protein 2 homolog / SAE2


Mass: 15273.274 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct expresses amino acids 31 to 145 of human CtIP. It contains two single-point mutations: C89 and C92 have been mutated to alanine. The GSMG peptide at the N-terminus contains the ...Details: The construct expresses amino acids 31 to 145 of human CtIP. It contains two single-point mutations: C89 and C92 have been mutated to alanine. The GSMG peptide at the N-terminus contains the amino acids left over after TEV cleavage of the MBP tag, and is not part of the CtIP sequence. The WSHPQFEK sequence at the C-terminus represents the Strep tag peptide and is not part of the CtIP sequence.,The construct expresses amino acids 31 to 145 of human CtIP. It contains two single-point mutations: C89 and C92 have been mutated to alanine. The GSMG peptide at the N-terminus contains the amino acids left over after TEV cleavage of the MBP tag, and is not part of the CtIP sequence. The WSHPQFEK sequence at the C-terminus represents the Strep tag peptide and is not part of the CtIP sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP8, CTIP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q99708, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Condition F6 of the Morpheus crystallisation screen MD-47 (Molecular Dimensions).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.802→37.5 Å / Num. obs: 8624 / % possible obs: 97.95 % / Redundancy: 2.8 % / Biso Wilson estimate: 79.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05463 / Rpim(I) all: 0.03947 / Rrim(I) all: 0.06769 / Net I/σ(I): 12.18
Reflection shellResolution: 2.802→2.902 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.7581 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 878 / CC1/2: 0.601 / Rpim(I) all: 0.5435 / Rrim(I) all: 0.9365 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology models

Resolution: 2.802→37.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2528 813 10 %
Rwork0.2235 --
obs-8612 97.95 %
Displacement parametersBiso max: 186.96 Å2 / Biso mean: 101.8615 Å2 / Biso min: 44.17 Å2
Refinement stepCycle: LAST / Resolution: 2.802→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 36 1893

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