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- PDB-5kgf: Structural model of 53BP1 bound to a ubiquitylated and methylated... -

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Entry
Database: PDB / ID: 5kgf
TitleStructural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution
Components
  • (DNA (145-MER)) x 2
  • Histone H2A type 1
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3.2
  • Histone H4
  • Tumor suppressor p53-binding protein 1
  • Ubiquitin
KeywordsSTRUCTURAL PROTEIN/DNA / DNA / chromatin / 53BP1 / STRUCTURAL PROTEIN-DNA complex
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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope ...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 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / telomeric DNA binding / virus tail / : / histone reader activity / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / DNA damage checkpoint signaling / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / replication fork / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription coregulator activity / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / protein homooligomerization / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / kinetochore / Meiotic recombination / double-strand break repair via nonhomologous end joining / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / UCH proteinases / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / p53 binding / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / site of double-strand break / heterochromatin formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / histone binding / damaged DNA binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / nuclear body / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular space / DNA binding / extracellular exosome / nucleoplasm / identical protein binding
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / breast cancer carboxy-terminal domain / Pectin lyase fold ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / breast cancer carboxy-terminal domain / Pectin lyase fold / Pectin lyase fold/virulence factor / BRCT domain profile. / BRCT domain / BRCT domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Tumor protein p53 binding protein 1 / Histone H2A type 1 / Tail fiber / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2 / TP53-binding protein 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsWilson, M.D. / Benlekbir, S. / Sicheri, F. / Rubinstein, J.L. / Durocher, D.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN143343 Canada
Canadian Institutes of Health Research (CIHR)MOP81294 Canada
Canadian Institutes of Health Research (CIHR)FDN143277 Canada
CitationJournal: Nature / Year: 2016
Title: The structural basis of modified nucleosome recognition by 53BP1.
Abstract: DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases ...DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates H2A on lysine 13 and lysine 15 (refs 7, 8) (yielding H2AK13ub and H2AK15ub, respectively), an event that triggers the recruitment of 53BP1 (also known as TP53BP1) to chromatin flanking DSBs. 53BP1 binds specifically to H2AK15ub-containing nucleosomes through a peptide segment termed the ubiquitination-dependent recruitment motif (UDR), which requires the simultaneous engagement of histone H4 lysine 20 dimethylation (H4K20me2) by its tandem Tudor domain. How 53BP1 interacts with these two histone marks in the nucleosomal context, how it recognizes ubiquitin, and how it discriminates between H2AK13ub and H2AK15ub is unknown. Here we present the electron cryomicroscopy (cryo-EM) structure of a dimerized human 53BP1 fragment bound to a H4K20me2-containing and H2AK15ub-containing nucleosome core particle (NCP-ubme) at 4.5 Å resolution. The structure reveals that H4K20me2 and H2AK15ub recognition involves intimate contacts with multiple nucleosomal elements including the acidic patch. Ubiquitin recognition by 53BP1 is unusual and involves the sandwiching of the UDR segment between ubiquitin and the NCP surface. The selectivity for H2AK15ub is imparted by two arginine fingers in the H2A amino-terminal tail, which straddle the nucleosomal DNA and serve to position ubiquitin over the NCP-bound UDR segment. The structure of the complex between NCP-ubme and 53BP1 reveals the basis of 53BP1 recruitment to DSB sites and illuminates how combinations of histone marks and nucleosomal elements cooperate to produce highly specific chromatin responses, such as those elicited following chromosome breaks.
History
DepositionJun 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection / Database references
Category: citation / em_software / pdbx_audit_support
Item: _citation.journal_id_CSD / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.5Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.7Nov 13, 2024Group: Data collection / Structure summary / Category: em_admin / em_entity_assembly_molwt / Item: _em_admin.last_update / _em_entity_assembly_molwt.id

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Structure visualization

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 1-C/E/F/G/I
I: DNA (145-MER)
J: DNA (145-MER)
L: Tumor suppressor p53-binding protein 1
O: Ubiquitin
M: Ubiquitin
K: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)221,34214
Polymers221,34214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area64290 Å2
ΔGint-390 kcal/mol
Surface area85630 Å2

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Components

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Protein , 5 types, 10 molecules AEBFCGDHOM

#1: Protein Histone H3.2 / Histone H3


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4 / Histone H4Kc20me2


Mass: 11439.511 Da / Num. of mol.: 2 / Mutation: K20C
Source method: isolated from a genetically manipulated source
Details: cysteine alkylation at position 20 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Details (production host): pDD2349 / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1 / H2A.1 / Histone H2A/p


Mass: 14163.539 Da / Num. of mol.: 2 / Mutation: K13R, T16S, K36R
Source method: isolated from a genetically manipulated source
Details: Isopeptide amide crosslink between K15 of H2A and G76 of ubiquitin
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2AG, H2AFP, HIST1H2AI, H2AFC, HIST1H2AK, H2AFD, HIST1H2AL, H2AFI, HIST1H2AM, H2AFN
Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S8
#4: Protein Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13937.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Escherichia coli (E. coli) / References: UniProt: P62807
#8: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 2 molecules LK

#7: Protein/peptide Tumor suppressor p53-binding protein 1


Mass: 2376.757 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: full protein not modeled / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: H7BZY0, UniProt: Q12888*PLUS

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1NCP-ubme/GST-53BP1 complexCOMPLEXSingle-particle electrocryomicroscopy structure of Tandem Tudor domain and UDR region of human 53BP1 bound to a recombinant ubiquitylated and methylated nucleosome core particle#1-#90MULTIPLE SOURCES
2NCP-ubmeCOMPLEXModified nucleosome core particle, H2A enzymatically ubiquitylated on H2A K15, H4 chemically alkylated at K20C to create dimethyl lysine analog#1-#6, #91MULTIPLE SOURCES
3Widom-601 DNACOMPLEX145 bp fragment of Widom-601 strong nuclesome positioning sequence, gift from Curt Davey (Vasudevan et. al, 2010, J.Mol.Biol.)#5-#62RECOMBINANT
4GST-53BP1COMPLEX53BP1 Tandem Tudor domain and ubiquitin dependent recruitment region, artificially dimerized with Gluthaione-S-transferase (GST, not visible in structure)#7-#81RECOMBINANT
5Ubiquitylated methylated histone octamerCOMPLEX#1-#4, #92MULTIPLE SOURCES
6Histone H4kc20Me2COMPLEXDimethylated at position 20#25RECOMBINANT
7Histone H3COMPLEX#15RECOMBINANT
8Histone H2B.1COMPLEX#45RECOMBINANT
9Histone H2A.1 K13RK36RCOMPLEXCrosslinked at H2AK15 to ubiquitin at ub G76 (isopeptide bond)#35RECOMBINANT
10UbiquitinCOMPLEXCrosslinked to H2A K15 (isopeptide bond)#95RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.318 MDaYES
220.226 MDaNO
330.88231 MDaNO
440.0892 MDaYES
550.138 MDaNO
66
77
88
99
1010
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12unclassified (unknown)32644
23synthetic construct (others)32630
34Homo sapiens (human)9606
45unclassified (unknown)32644
56Xenopus laevis (African clawed frog)8355
67Xenopus laevis (African clawed frog)8355
78Homo sapiens (human)9606
89Homo sapiens (human)9606
910Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
12unclassified (unknown)32644unknown
23Escherichia coli (E. coli)562pUC57-8x145bp
34Escherichia coli (E. coli)562pDD2621
45unclassified (unknown)32644unknown
56Escherichia coli (E. coli)562pDD2349
67Escherichia coli (E. coli)562pDD1874
78Escherichia coli (E. coli)562pDD2644
89Escherichia coli (E. coli)562pDD2647
910Escherichia coli (E. coli)562pDD2528
Buffer solutionpH: 7.5
Details: High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
230 mMpotassium chlorideKCl1
30.5 mMEDTA1
41 mMDTT1
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: electron micrsocopy sciences
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Plunged into liquid ethane-propane (FEI VITROBOT MARK III)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 25000 X / Calibrated magnification: 34483 X / Cs: 2 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 319
Image scansMovie frames/image: 30 / Used frames/image: 1-30

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
2DigitalMicrograph2.31.691.0image acquisition
4CTFFIND3CTF correction
7UCSF Chimera1.10.1model fitting
9PHENIX1.10.1.2115model refinement
10RELION1.3initial Euler assignment
11RELION1.3final Euler assignment
12RELION1.3classification
13RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 174185
Details: Automatically picked from roughly 3000 particles using a manually picked template
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45361 / Algorithm: FOURIER SPACE / Num. of class averages: 9 / Symmetry type: POINT
Atomic model buildingB value: 207.5 / Protocol: RIGID BODY FIT / Space: REAL
Details: The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing ...Details: The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing flexibility into the 3D maps using UCSF Chimera. Segmentation was performed in UCSF Chimera. For the NCP-ubme structure the ubiquitin segmentation was further modified to remove obvious NCP density from the ubiquitin segment. The H2A/H2B sequence was mutated to the human H2AK13R/K36R and H2B manually in UCSF Chimera. A polyalanine model of the UDR was built within the UDR density in Coot, which compared well to predicted structures generated by Rosetta. The UDR model was mutated and fitted using UCSF Chimera, followed by iterative rounds of real-space refinement in PHENIX and model optimization in Coot. All figures were prepared in UCSF Chimera.
RefinementHighest resolution: 4.54 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00914660
ELECTRON MICROSCOPYf_angle_d0.96321001
ELECTRON MICROSCOPYf_dihedral_angle_d20.8749872
ELECTRON MICROSCOPYf_chiral_restr0.0632391
ELECTRON MICROSCOPYf_plane_restr0.0061659

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