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- PDB-4d2h: Crystal structure of the tetramerisation domain of human CtIP -

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Basic information

Entry
Database: PDB / ID: 4d2h
TitleCrystal structure of the tetramerisation domain of human CtIP
ComponentsRBBP8
KeywordsGENE REGULATION / CTIP/RBBP8 / DOUBLE-STRAND DNA BREAK REPAIR / DNA-END RESECTION / GENE CONVERSION / HOMOLOGOUS RECOMBINATION
Function / homology
Function and homology information


DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / blastocyst hatching / single-stranded DNA endodeoxyribonuclease activity / DNA strand resection involved in replication fork processing / homologous recombination / HDR through MMEJ (alt-NHEJ) / Impaired BRCA2 binding to PALB2 / mitotic G2/M transition checkpoint / Defective homologous recombination repair (HRR) due to BRCA1 loss of function ...DNA double-strand break processing involved in repair via single-strand annealing / BRCA1-C complex / blastocyst hatching / single-stranded DNA endodeoxyribonuclease activity / DNA strand resection involved in replication fork processing / homologous recombination / HDR through MMEJ (alt-NHEJ) / Impaired BRCA2 binding to PALB2 / mitotic G2/M transition checkpoint / 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 / Homologous DNA Pairing and Strand Exchange / 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 / G1/S transition of mitotic cell cycle / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Meiotic recombination / transcription corepressor activity / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / Hydrolases; Acting on ester bonds / cell division / DNA repair / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus
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: 1.9 Å
AuthorsDavies, O.R. / Sun, M. / Pellegrini, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Ctip Tetramer Assembly is Required for DNA-End Resection and Repair.
Authors: Davies, O.R. / Forment, J.V. / Sun, M. / Belotserkovskaya, R. / Coates, J. / Galanty, Y. / Demir, M. / Morton, C.R. / Rzechorzek, N.J. / Jackson, S.P. / Pellegrini, L.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / atom_site_anisotrop / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RBBP8
B: RBBP8
C: RBBP8
D: RBBP8
E: RBBP8
F: RBBP8
G: RBBP8
H: RBBP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,44322
Polymers36,0988
Non-polymers1,34514
Water2,468137
1
E: RBBP8
F: RBBP8
G: RBBP8
H: RBBP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,81712
Polymers18,0494
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-152.3 kcal/mol
Surface area9690 Å2
MethodPISA
2
A: RBBP8
B: RBBP8
C: RBBP8
D: RBBP8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,62510
Polymers18,0494
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-147.2 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.970, 37.910, 97.790
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
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: 4512.235 Da / Num. of mol.: 8 / Fragment: TETRAMERISATION DOMAIN, RESIDUES 18-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMAT11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q99708, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.86 Å3/Da / Density % sol: 36.3 % / Description: NONE
Crystal growDetails: 200 MM LITHIUM SULPHATE, 100 MM SODIUM ACETATE PH 3.6, 32% (V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0397
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 1.9→28.98 Å / Num. obs: 20994 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.16 Å / Cor.coef. Fo:Fc: 0.9349 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.164
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1079 5.15 %RANDOM
Rwork0.2122 ---
obs0.2144 20969 99.4 %-
Displacement parametersBiso mean: 49.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.1078 Å20 Å20.4275 Å2
2---5.4139 Å20 Å2
3---5.5217 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 70 137 2474
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014703HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.888552HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1107SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes623HARMONIC5
X-RAY DIFFRACTIONt_it4703HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion14.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4747SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2294 136 4.9 %
Rwork0.2164 2642 -
all0.217 2778 -
obs--99.4 %
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)
11.7067-0.3173-0.47090.8468-3.006313.8012-0.07510.4117-0.1381-0.29850.1932-0.23350.3318-0.1157-0.1180.2053-0.07480.08480.08-0.0325-0.22363.4807-1.72889.7623
22.37030.31132.02362.4515-0.15827.6394-0.0575-0.13920.09910.5208-0.0601-0.43780.04890.19260.1176-0.05240.0318-0.1298-0.1508-0.0527-0.21775.07932.016236.9078
30.38070.2005-1.30831.55-1.58644.8291-0.022-0.0844-0.0734-0.08950.03740.05170.4498-0.2257-0.0154-0.0693-0.0292-0.03330.12110.0077-0.1857-4.089-5.460341.6799
40.9232-0.21962.16180.6906-1.05869.52470.04-0.0652-0.0229-0.24710.03260.1167-0.2366-0.4973-0.07270.08950.0779-0.07490.0776-0.001-0.1379-4.98764.880611.0018
51.6474-0.6549-0.90860.76890.20428.6547-0.0217-0.3968-0.00150.01930.1747-0.0077-0.46010.4258-0.1530.00460.0335-0.06340.06970.0056-0.268822.6118-16.138135.4284
60.90940.2972-0.5990.44460.07191.95230.07130.2117-0.0411-0.08420.0028-0.11210.13870.2058-0.0740.12870.1529-0.09840.1191-0.0597-0.257523.4812-20.851411.8281
70.55440.301-0.35660.8686-0.9316.8575-0.13630.1916-0.0542-0.47090.14060.1061-0.3138-0.6478-0.00420.24360.0312-0.13490.119-0.0483-0.223314.3363-13.49188.7485
80.4081-0.1870.28240.8057-0.4944.41010.0036-0.0944-0.1149-0.2434-0.09860.1430.0797-0.450.095-0.02890.0304-0.11820.0574-0.0535-0.180713.6081-23.562133.8882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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