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- PDB-9ckj: Co-crystal structure of 53BP1 tandem Tudor domains in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9ckj
TitleCo-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512
ComponentsTP53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 / UNC9512 / Structural Genomics / PSI-Biology / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of isotype switching / negative regulation of double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / kinetochore / site of double-strand break / nuclear body / regulation of DNA-templated transcription / DNA binding / nucleoplasm
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
: / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZeng, H. / Dong, A. / Shell, D.J. / Foley, C. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512
Authors: Zeng, H. / Dong, A. / Shell, D.J. / Foley, C. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionJul 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TP53-binding protein 1
B: TP53-binding protein 1
C: TP53-binding protein 1
D: TP53-binding protein 1
E: TP53-binding protein 1
F: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,62114
Polymers84,3896
Non-polymers3,2328
Water3,531196
1
A: TP53-binding protein 1
B: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2074
Polymers28,1302
Non-polymers1,0772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TP53-binding protein 1
D: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2074
Polymers28,1302
Non-polymers1,0772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: TP53-binding protein 1
F: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2076
Polymers28,1302
Non-polymers1,0774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.884, 76.025, 258.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
TP53-binding protein 1


Mass: 14064.842 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NNK5
#2: Chemical
ChemComp-A1AY8 / (3S)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]-N-[(3M)-3-(3-oxo-2,3-dihydro-1H-isoindol-5-yl)phenyl]piperidine-3-carboxamide


Mass: 538.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H34N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 39221 / % possible obs: 97.9 % / Redundancy: 6.9 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.048 / Rrim(I) all: 0.128 / Χ2: 2.727 / Net I/σ(I): 11.1 / Num. measured all: 270070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.294.40.54816390.7290.9180.2680.6141.22282.9
2.29-2.335.20.50317730.7930.9410.2330.5571.19191.1
2.33-2.386.10.47919250.8320.9530.2070.5241.20398.7
2.38-2.426.90.46619450.8640.9630.1880.5041.28499.3
2.42-2.487.40.42519730.8970.9720.1670.4581.32299.2
2.48-2.537.40.41119420.9160.9780.1620.4431.41499.2
2.53-2.67.50.37619690.9060.9750.1470.4051.50299.3
2.6-2.677.40.33819400.9370.9840.1330.3641.65599.4
2.67-2.757.50.28719810.9470.9860.1130.3091.91399.2
2.75-2.837.40.24119390.9590.9890.0940.2592.23599.3
2.83-2.947.40.20119820.9690.9920.0790.2162.61799.3
2.94-3.057.30.18119790.9720.9930.0720.1962.95399.2
3.05-3.197.20.15219890.9710.9930.0610.1643.50799
3.19-3.367.10.13319460.980.9950.0540.1444.18998.9
3.36-3.5770.12320080.9840.9960.050.1334.61199.1
3.57-3.856.90.11120000.9830.9960.0460.1215.05199.1
3.85-4.236.90.09920070.980.9950.0420.1075.04399
4.23-4.856.80.08620340.9910.9980.0360.0934.47399.5
4.85-6.16.90.08220740.9910.9980.0340.0893.36199.4
6.1-506.50.05521760.99810.0230.062.41597.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.92 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.315 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1892 4.83 %RANDOM
Rwork0.219 ---
obs0.221 39150 97.5 %-
Displacement parametersBiso mean: 48.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.1261 Å20 Å20 Å2
2--0.5231 Å20 Å2
3----1.6493 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.25→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 242 196 5966
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015926HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.078022HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2036SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1085HARMONIC5
X-RAY DIFFRACTIONt_it5926HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion16.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion686SEMIHARMONIC5
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_contact6514SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.28 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2909 -4.09 %
Rwork0.2693 751 -
all0.2702 783 -
obs--69.14 %
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)
11.92930.2387-0.56822.70970.8473.79410.0168-0.0020.02330.07410.02470.10340.1187-0.1218-0.04150.0648-0.019-0.0171-0.1923-0.0031-0.127224.384640.11774.0106
21.06370.04620.71073.1660.57172.26820.0895-0.1033-0.02690.1815-0.1383-0.15870.02360.0330.04890.1161-0.0069-0.0157-0.1435-0.0008-0.095631.901458.630322.8404
31.6649-0.4568-0.25731.39910.12741.8956-0.0379-0.06570.10410.02960.04590.10490.11150.0107-0.0080.06090.0021-0.0366-0.1466-0.0112-0.02244.287813.692917.6186
44.0827-0.34970.73152.0202-0.43886.8422-0.0179-0.27120.25810.21070.2424-0.17-0.26390.1151-0.22450.02210.0409-0.0956-0.211-0.1338-0.170713.856527.720638.9403
53.37420.58622.56267.1836-2.22147.29450.1429-0.06380.0545-0.25670.1076-0.0307-0.08450.0754-0.25050.1079-0.0129-0.1216-0.2165-0.0419-0.309216.7826-5.035867.2747
62.5691-0.1110.55236.14680.01415.55530.0101-0.39920.17160.2606-0.01740.0865-0.0906-0.41310.00740.1018-0.0748-0.0815-0.21710.0252-0.30751.8793-7.354543.8681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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