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- EMDB-41707: Cryo-EM structure of the human nucleosome core particle ubiquityl... -

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Entry
Database: EMDB / ID: EMD-41707
TitleCryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)
Map data
Sample
  • Complex: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Histone H2A type 1-B/E
KeywordsNucleosome 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 / double-strand break repair via classical nonhomologous end joining / isotype switching / symbiont entry into host cell via disruption of host cell glycocalyx / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / symbiont entry into host cell via disruption of host cell envelope / virus tail / DNA repair-dependent chromatin remodeling ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / double-strand break repair via classical nonhomologous end joining / isotype switching / symbiont entry into host cell via disruption of host cell glycocalyx / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / symbiont entry into host cell via disruption of host cell envelope / virus tail / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / ubiquitin ligase complex / interstrand cross-link repair / SUMOylation of DNA damage response and repair proteins / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / nucleosome binding / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ubiquitin binding / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / RING-type E3 ubiquitin transferase / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / 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 / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / 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 / double-strand break repair / 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) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / histone binding / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / protein ubiquitination / defense response to Gram-positive bacterium / cadherin binding
Similarity search - Function
E3 ubiquitin-protein ligase RNF168 / : / Prokaryotic RING finger family 4 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ring finger / : / Histone H2B signature. ...E3 ubiquitin-protein ligase RNF168 / : / Prokaryotic RING finger family 4 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ring finger / : / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2A type 1-B/E / Tail fiber / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHu Q / Botuyan MV / Zhao D / Cui G / Mer G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: 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
DepositionAug 24, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41707.png

Downloads & links

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Map

FileDownload / File: emd_41707.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å		1.33 Å/pix.
x 256 pix.
= 339.968 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.042203907 - 0.07382913
Average (Standard dev.)0.00007830605 (±0.0016209423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41707_msk_1.map
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Additional map: #1

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Half map: #1

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Sample components

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Entire : Human nucleosome core particle ubiquitylated at histone H2A K15 i...

EntireName: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)
Components
  • Complex: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
    • Protein or peptide: Polyubiquitin-B
    • Protein or peptide: Histone H2A type 1-B/E

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Supramolecule #1: Human nucleosome core particle ubiquitylated at histone H2A K15 i...

SupramoleculeName: Human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.786534 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.743792 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.084348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMPEPAK SAPAPKKGSK KAVTKAQKKD GKKRKRSRKE SYSIYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTS

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #6: E3 ubiquitin-protein ligase RNF168

MacromoleculeName: E3 ubiquitin-protein ligase RNF168 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.16818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #7: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.057391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMMQIFV KTLTGKTITL EVEPSDTIEN VKAKIQDKEG IPPDQQRLIF AGKQLEDGRT LSDYNIQKES TLHLVLRLRG G

UniProtKB: Tail fiber

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Macromolecule #8: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.992091 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SASAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (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)

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.610043 KDa
SequenceString: (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)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9619981
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 47733
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0.7)

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Atomic model buiding 1

Initial model
PDB IDChain

7lya

source_name: PDB, initial_model_type: experimental model

1ubq

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8txw:
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)

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