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- EMDB-41708: Cryo-EM structure of the human nucleosome core particle ubiquityl... -
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Open data
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Basic information
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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) | |||||||||
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Function / homology | ![]() histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / double-strand break repair via classical nonhomologous end joining / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hu Q / Botuyan MV / Zhao D / Cui G / Mer G | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.9 KB 27.9 KB | Display Display | ![]() |
Images | ![]() | 125.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() ![]() | 37.6 MB 49.8 MB 49.8 MB | ||
Archive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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-Additional map: #1
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-Half map: #1
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Density Histograms |
-Half map: #2
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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: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 15.786534 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GPGHMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A UniProtKB: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 11.743792 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GPGHMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG UniProtKB: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 14.084348 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 66.16818 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 9.057391 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 12.992091 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
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: ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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. |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 9619981 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) |
Final 3D classification | Number classes: 3 / Software - Name: RELION (ver. 3.0.7) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 35548 |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | ![]() PDB-8txx: |