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Yorodumi- EMDB-41708: Cryo-EM structure of the human nucleosome core particle ubiquityl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41708 | |||||||||
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Title | Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nucleosome core particle / chromatin / RNF168 / MIU2-LRM domains / DNA repair / DNA double-strand break / Homologous recombination / BRCA1-BARD1 / 53BP1 / ubiquitin / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex / TRANSFERASE | |||||||||
Function / homology | Function and homology information histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / DNA repair-dependent chromatin remodeling / mitochondrion transport along microtubule / fat pad development ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / DNA repair-dependent chromatin remodeling / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / negative regulation of transcription elongation by RNA polymerase II / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / nucleosome binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / regulation of neuron apoptotic process / Chromatin modifying enzymes / interstrand cross-link repair / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / SUMOylation of DNA damage response and repair proteins / regulation of proteasomal protein catabolic process / Packaging Of Telomere Ends / ubiquitin ligase complex / energy homeostasis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / Maturation of protein E / ER Quality Control Compartment (ERQC) / nucleosomal DNA binding / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Inhibition of DNA recombination at telomere / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / telomere organization / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Meiotic synapsis / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / positive regulation of DNA repair / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / epigenetic regulation of gene expression / Regulation of pyruvate metabolism / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Downregulation of ERBB2:ERBB3 signaling / Assembly of the ORC complex at the origin of replication / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Translesion synthesis by POLK / neuron projection morphogenesis / Condensation of Prophase Chromosomes / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Hu Q / Botuyan MV / Zhao D / Cui G / Mer G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Authors: Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer / Abstract: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for ...RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41708.map.gz | 4.2 MB | EMDB map data format | |
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Header (meta data) | emd-41708-v30.xml emd-41708.xml | 27.9 KB 27.9 KB | Display Display | EMDB header |
Images | emd_41708.png | 125.7 KB | ||
Masks | emd_41708_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-41708.cif.gz | 7.6 KB | ||
Others | emd_41708_additional_1.map.gz emd_41708_half_map_1.map.gz emd_41708_half_map_2.map.gz | 37.6 MB 49.8 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41708 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41708 | HTTPS FTP |
-Validation report
Summary document | emd_41708_validation.pdf.gz | 767.8 KB | Display | EMDB validaton report |
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Full document | emd_41708_full_validation.pdf.gz | 767.4 KB | Display | |
Data in XML | emd_41708_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_41708_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41708 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41708 | HTTPS FTP |
-Related structure data
Related structure data | 8txxMC 8smwC 8smxC 8smyC 8smzC 8sn0C 8sn1C 8sn2C 8sn3C 8sn4C 8sn5C 8sn6C 8sn7C 8sn8C 8sn9C 8snaC 8txvC 8txwC 8u13C 8u14C 8upfC 8uq8C 8uq9C 8uqaC 8uqbC 8uqcC 8uqdC 8uqeC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41708.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41708_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_41708_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41708_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41708_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human nucleosome core particle ubiquitylated at histone H2A K15 i...
Entire | Name: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) |
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Components |
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-Supramolecule #1: Human nucleosome core particle ubiquitylated at histone H2A K15 i...
Supramolecule | Name: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 280 KDa |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.786534 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGHMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A UniProtKB: Histone H3.1 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.743792 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGHMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2B type 1-C/E/F/G/I
Macromolecule | Name: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.084348 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGHMPEPAK SAPAPKKGSK KAVTKAQKKD GKKRKRSRKE SYSIYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTS UniProtKB: Histone H2B type 1-C/E/F/G/I |
-Macromolecule #6: E3 ubiquitin-protein ligase RNF168
Macromolecule | Name: E3 ubiquitin-protein ligase RNF168 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66.16818 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGMALPKDA IPSLSECQCG ICMEILVEPV TLPCNHTLCK PCFQSTVEKA SLCCPFCRRR VSSWTRYHTR RNSLVNVELW TIIQKHYPR ECKLRASGQE SEEVADDYQP VRLLSKPGEL RREYEEEISK VAAERRASEE EENKASEEYI QRLLAEEEEE E KRQAEKRR ...String: GPGMALPKDA IPSLSECQCG ICMEILVEPV TLPCNHTLCK PCFQSTVEKA SLCCPFCRRR VSSWTRYHTR RNSLVNVELW TIIQKHYPR ECKLRASGQE SEEVADDYQP VRLLSKPGEL RREYEEEISK VAAERRASEE EENKASEEYI QRLLAEEEEE E KRQAEKRR RAMEEQLKSD EELARKLSID INNFCEGSIS ASPLNSRKSD PVTPKSEKKS KNKQRNTGDI QKYLTPKSQF GS ASHSEAV QEVRKDSVSK DIDSSDRKSP TGQDTEIEDM PTLSPQISLG VGEQGADSSI ESPMPWLCAC GAEWYHEGNV KTR PSNHGK ELCVLSHERP KTRVPYSKET AVMPCGRTES GCAPTSGVTQ TNGNNTGETE NEESCLLISK EISKRKNQES SFEA VKDPC FSAKRRKVSP ESSPDQEETE INFTQKLIDL EHLLFERHKQ EEQDRLLALQ LQKEVDKEQM VPNRQKGSPD EYHLR ATSS PPDKVLNGQR KNPKDGNFKR QTHTKHPTPE RGSRDKNRQV SLKMQLKQSV NRRKMPNSTR DHCKVSKSAH SLQPSI SQK SVFQMFQRCT KHHHHHH UniProtKB: E3 ubiquitin-protein ligase RNF168 |
-Macromolecule #7: Polyubiquitin-B
Macromolecule | Name: Polyubiquitin-B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 9.057391 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGHMMQIFV KTLTGKTITL EVEPSDTIEN VKAKIQDKEG IPPDQQRLIF AGKQLEDGRT LSDYNIQKES TLHLVLRLRG G UniProtKB: Polyubiquitin-B |
-Macromolecule #8: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.992091 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SASAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #4: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.13877 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT) |
-Macromolecule #5: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.610043 KDa |
Sequence | String: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | 10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11712 / Average electron dose: 50.0 e/Å2 Details: 11712 images were recorded in movie-mode of which 10993 were retained for particle picking. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | PDB-8txx: |