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- PDB-4cri: Crystal Structure of 53BP1 tandem tudor domains in complex with m... -

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Basic information

Entry
Database: PDB / ID: 4cri
TitleCrystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide
Components
  • RB1 PROTEIN
  • TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
KeywordsPEPTIDE BINDING PROTEIN / TUMOUR SUPPRESSOR PRB / 53BP1
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / ubiquitin-modified histone reader activity / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / positive regulation of isotype switching / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of centromere complex assembly / positive regulation of macrophage differentiation / cellular response to X-ray / glial cell apoptotic process / tissue homeostasis / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / double-strand break repair via classical nonhomologous end joining / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / protein localization to site of double-strand break / neuron maturation / digestive tract development / aortic valve morphogenesis / DNA repair complex / Replication of the SARS-CoV-1 genome / myoblast differentiation / negative regulation of cold-induced thermogenesis / SWI/SNF complex / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / telomeric DNA binding / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / hepatocyte apoptotic process / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of apoptotic signaling pathway / transcription factor binding / SUMOylation of transcription factors / negative regulation of cell cycle / chromosome organization / glial cell proliferation / negative regulation of double-strand break repair via homologous recombination / chondrocyte differentiation / Nuclear events stimulated by ALK signaling in cancer / heterochromatin formation / Cyclin E associated events during G1/S transition / negative regulation of smoothened signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / methylated histone binding / histone reader activity / Condensation of Prophase Chromosomes / epithelial cell proliferation / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / phosphoprotein binding / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / G2/M DNA damage checkpoint / protein homooligomerization / Oncogene Induced Senescence / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body / kinetochore / kinase binding / positive regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / double-strand break repair via nonhomologous end joining / spindle / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / transcription corepressor activity / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / neuron projection development / disordered domain specific binding / p53 binding / cellular response to xenobiotic stimulus / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Replication of the SARS-CoV-2 genome / Processing of DNA double-strand break ends / histone binding
Similarity search - Function
: / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) ...: / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / : / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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
Retinoblastoma-associated protein / RB1 protein / TP53-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKrojer, T. / Johansson, C. / Gileadi, C. / Fedorov, O. / Carr, S. / La Thangue, N.B. / Vollmar, M. / Crawley, L. / von Delft, F. / Bountra, C. ...Krojer, T. / Johansson, C. / Gileadi, C. / Fedorov, O. / Carr, S. / La Thangue, N.B. / Vollmar, M. / Crawley, L. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Lysine Methylation-Dependent Binding of 53BP1 to the Prb Tumor Suppressor.
Authors: Carr, S.M. / Munro, S. / Zalmas, L. / Fedorov, O. / Johansson, C. / Krojer, T. / Sagum, C.A. / Bedford, M.T. / Oppermann, U. / La Thangue, N.B.
History
DepositionFeb 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
B: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
C: RB1 PROTEIN
D: RB1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,7784
Polymers42,7784
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-18.4 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.789, 105.789, 156.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TUMOR SUPPRESSOR P53-BINDING PROTEIN 1 / 53BP1 / P53-BINDING PROTEIN 1 / P53BP1 / 53BP1


Mass: 19447.787 Da / Num. of mol.: 2 / Fragment: TANDEM TUDOR DOMAIN, RESIDUES 1459-1634
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12888
#2: Protein/peptide RB1 PROTEIN / RBK810ME2 PEPTIDE


Mass: 1941.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P78495, UniProt: P06400*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.43 Å3/Da / Density % sol: 58.28 % / Description: NONE
Crystal growpH: 7.5
Details: 5%(W/V) PEG10K. 0.15M MAGNESIUM CHLORIDE, 0.1M TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→52.05 Å / Num. obs: 22195 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 59.65 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LH0

3lh0


Resolution: 2.35→39.51 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1159 5.2 %
Rwork0.1943 --
obs0.196 22129 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 0 23 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012008
X-RAY DIFFRACTIONf_angle_d1.3292705
X-RAY DIFFRACTIONf_dihedral_angle_d14.403731
X-RAY DIFFRACTIONf_chiral_restr0.055287
X-RAY DIFFRACTIONf_plane_restr0.006343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.4570.33381570.29122526X-RAY DIFFRACTION99
2.457-2.58650.34921250.27632579X-RAY DIFFRACTION100
2.5865-2.74860.32931740.26312521X-RAY DIFFRACTION100
2.7486-2.96070.27141510.23382584X-RAY DIFFRACTION100
2.9607-3.25850.27031470.23412597X-RAY DIFFRACTION100
3.2585-3.72970.25631170.21242648X-RAY DIFFRACTION100
3.7297-4.69790.17431480.15272665X-RAY DIFFRACTION100
4.6979-39.51540.2011400.17282850X-RAY DIFFRACTION100
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)
10.8090.5233-0.38481.07740.47021.11840.2105-0.25170.00470.4754-0.2908-0.56960.3059-0.3508-0.00070.5376-0.1053-0.13920.38240.12060.5143-35.674925.236523.0081
20.960.67910.66391.26840.31940.62620.4713-0.3526-0.03880.478-0.2179-0.8805-0.0658-0.11320.00040.6617-0.1335-0.18030.58540.16220.6825-33.278728.076226.3215
30.06290.11380.01860.1940.0349-0.0053-0.128-0.0918-0.42370.0741-0.1220.22950.3418-0.09080.00050.7513-0.1528-0.05590.50790.10920.5933-44.306117.836618.1859
40.3043-0.20260.14190.4329-0.33250.2328-0.10080.3915-0.3474-0.22940.0164-0.02170.3104-0.5084-0.00010.5806-0.13910.0460.46270.02390.483-41.180528.11463.9351
50.36770.2988-0.03210.2307-0.02790.199-0.31460.1995-0.0986-0.9792-0.1773-0.1660.6994-0.3739-0.02350.7775-0.15130.14820.30750.06180.5229-43.094315.49047.9465
60.16160.046-0.35110.3712-0.10580.7218-0.1795-0.2078-0.5019-1.47650.21450.01650.32650.06030.00080.8848-0.05360.07420.50320.0280.6277-39.521115.97987.0523
70.44850.2846-0.29021.2671-0.74380.4569-0.25580.00220.0279-0.35520.0701-0.50730.7377-0.4110.01770.7269-0.10320.07560.4663-0.00080.4143-41.447320.66196.0371
80.20660.2394-0.22910.447-0.07210.32060.117-0.2168-0.00480.6642-0.04320.17110.3139-1.11060.00020.5753-0.16390.02970.60740.05820.5188-48.701624.804722.6441
90.1236-0.0667-0.06410.03290.03380.0274-0.6772-0.0457-0.21760.26190.0899-0.56010.51240.4991-0.00270.5232-0.11070.05960.54670.13920.5217-34.774131.75846.4773
100.41540.08750.64281.69470.11791.46310.7589-0.1322-0.91720.2124-0.4775-0.39450.5264-0.15770.00080.5581-0.1706-0.22350.65230.01990.6873-27.016842.375427.9619
110.2486-0.3149-0.0370.57130.50561.21920.904-0.22-0.7785-0.3412-0.4916-0.1374-0.75960.74410.06460.6304-0.0137-0.29710.74820.08050.8167-24.64837.898923.2302
120.4660.1045-0.45110.57150.2240.59110.5048-0.4542-0.50280.6302-0.5372-0.71860.1399-0.3819-0.00070.7831-0.2628-0.22140.70240.15950.6184-28.946638.460827.3962
131.3108-1.03160.08881.6136-0.22460.06830.819-0.63370.05610.3785-1.18140.04260.488-0.9235-0.15250.549-0.5926-0.02131.0739-0.20370.5769-32.886250.58837.4058
140.07470.0239-0.06150.3757-0.330.24470.0967-0.5979-0.50880.4525-0.28960.7359-0.0886-0.70090.00430.7579-0.4128-0.00971.0561-0.15510.8679-28.432355.718841.9309
151.2464-0.44340.16150.9083-0.71731.22910.06070.23090.10271.225-1.0253-0.12571.403-0.8632-0.02310.8919-0.5027-0.03671.0896-0.05530.6404-26.876952.452643.7417
161.81880.5904-0.73860.37860.10170.89190.9821-0.4342-0.05470.5795-0.394-0.0250.1115-0.96930.13580.8639-0.6844-0.06531.1448-0.11930.1867-32.497751.955442.0684
170.39230.17550.27390.22110.01110.26680.06470.1730.5971-0.6623-0.51980.2369-1.29220.152-0.00150.6737-0.1216-0.13880.8007-0.00650.788-31.970953.951524.5896
180.3661-0.38410.26450.4017-0.27390.18620.5175-0.4602-0.33820.2273-0.1057-0.311-0.07170.7560.01561.2768-0.8815-0.16171.19450.10550.7391-40.322840.649338.4482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1485 THROUGH 1509 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1510 THROUGH 1531 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1532 THROUGH 1542 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1543 THROUGH 1553 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1554 THROUGH 1564 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1565 THROUGH 1574 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 1575 THROUGH 1589 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 1590 THROUGH 1603 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 2001 THROUGH 2006 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1485 THROUGH 1509 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 1510 THROUGH 1519 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 1520 THROUGH 1531 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 1532 THROUGH 1553 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 1554 THROUGH 1564 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 1565 THROUGH 1574 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 1575 THROUGH 1589 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 1590 THROUGH 1603 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 2003 THROUGH 2006 )

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