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- PDB-8swj: Co-crystal structure of 53BP1 tandem Tudor domains in complex wit... -

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Entry
Database: PDB / ID: 8swj
TitleCo-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531
ComponentsTP53-binding protein 1
KeywordsTRANSCRIPTION / 53BP1 / tudor domain / tumor suppressor / TP53-BINDING PROTEIN 1 / SGC / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / : / histone reader activity ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / : / histone reader activity / SUMOylation of transcription factors / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of double-strand break repair via homologous recombination / DNA damage checkpoint signaling / replication fork / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-WWQ / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZeng, H. / Dong, A. / Shell, D.J. / Foley, C. / Pearce, K.H. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC8531
Authors: Zeng, H. / Dong, A. / Shell, D.J. / Foley, C. / Pearce, K.H. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionMay 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5949
Polymers56,4884
Non-polymers2,1075
Water4,522251
1
A: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6492
Polymers14,1221
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6492
Polymers14,1221
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6493
Polymers14,1221
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TP53-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6492
Polymers14,1221
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.159, 55.902, 78.522
Angle α, β, γ (deg.)90.00, 105.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TP53-binding protein 1 / p53BP1


Mass: 14121.893 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: BL21(DE3)-V2R-pRARE2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#2: Chemical
ChemComp-WWQ / (3S)-N-(4'-carbamoyl[1,1'-biphenyl]-3-yl)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]piperidine-3-carboxamide


Mass: 526.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H34N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Ammonium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→45.01 Å / Num. obs: 61582 / % possible obs: 99.2 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.023 / Rrim(I) all: 0.045 / Χ2: 0.58 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.658 / Num. measured all: 11366 / Num. unique obs: 3026 / CC1/2: 0.68 / Rpim(I) all: 0.395 / Rrim(I) all: 0.773 / Χ2: 0.62 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.535 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26176 3064 5 %RANDOM
Rwork0.21758 ---
obs0.21977 58501 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å20.19 Å2
2--0.11 Å2-0 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 157 251 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134141
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173797
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.6295597
X-RAY DIFFRACTIONr_angle_other_deg1.2631.6348753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98621.592201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92215668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3741526
X-RAY DIFFRACTIONr_chiral_restr0.0630.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02953
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8132.1872006
X-RAY DIFFRACTIONr_mcbond_other1.812.1862004
X-RAY DIFFRACTIONr_mcangle_it2.913.2712506
X-RAY DIFFRACTIONr_mcangle_other2.913.2712507
X-RAY DIFFRACTIONr_scbond_it1.9612.3792135
X-RAY DIFFRACTIONr_scbond_other1.962.3792136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0963.4773092
X-RAY DIFFRACTIONr_long_range_B_refined4.79824.8654418
X-RAY DIFFRACTIONr_long_range_B_other4.77224.7444382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 221 -
Rwork0.284 4336 -
obs--99.93 %

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