[English] 日本語
Yorodumi
- EMDB-34274: Bre1-nucleosome complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34274
TitleBre1-nucleosome complex
Map data3DFlex map
Sample
  • Complex: Bre1-nucleosome complex
    • Complex: Histone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA
      • DNA: DNA (147-mer)
      • DNA: DNA (147-mer)
    • Complex: Bre1
      • Protein or peptide: E3 ubiquitin-protein ligase BRE1A
      • Protein or peptide: E3 ubiquitin-protein ligase BRE1B
  • Ligand: ZINC ION
Keywordstranscription / ubiquitin ligase / cancer / chromatin / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / ubiquitin ligase complex ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / RHOBTB1 GTPase cycle / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / ubiquitin ligase complex / epigenetic regulation of gene expression / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / negative regulation of cell migration / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / mRNA 3'-UTR binding / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / protein polyubiquitination / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / UCH proteinases / ubiquitin protein ligase activity / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / p53 binding / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / histone binding / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / transcription coactivator activity / protein ubiquitination / Ub-specific processing proteases / neuron projection / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / ubiquitin protein ligase binding / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...E3 ubiquitin ligase Bre1 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase BRE1B / Histone H2B type 1-J / Histone H2A type 1 / Histone H4 / Histone H3.1 / E3 ubiquitin-protein ligase BRE1A
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsOnishi S / Hamada K / Sato K / Nishizawa T / Nureki O / Ogata K / Sengoku T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the human Bre1 complex bound to the nucleosome.
Authors: Shuhei Onishi / Kotone Uchiyama / Ko Sato / Chikako Okada / Shunsuke Kobayashi / Keisuke Hamada / Tomohiro Nishizawa / Osamu Nureki / Kazuhiro Ogata / Toru Sengoku /
Abstract: Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of ...Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of Bre1A/RNF20 and Bre1B/RNF40. The Bre1 proteins generally function as tumor suppressors, while in certain cancers, they facilitate cancer cell proliferation. To obtain structural insights of H2BK120 ubiquitination and its regulation, we report the cryo-electron microscopy structure of the human Bre1 complex bound to the nucleosome. The two RING domains of Bre1A and Bre1B recognize the acidic patch and the nucleosomal DNA phosphates around SHL 6.0-6.5, which are ideally located to recruit the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. Mutational experiments suggest that the two RING domains bind in two orientations and that ubiquitination occurs when Bre1A binds to the acidic patch. Our results provide insights into the H2BK120-specific ubiquitination by the Bre1 proteins and suggest that H2B monoubiquitination can be regulated by nuclesomal DNA flexibility.
History
DepositionSep 12, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34274.png

Downloads & links

-
Map

FileDownload / File: emd_34274.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3DFlex map
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.017542299 - 0.043336485
Average (Standard dev.)0.00004297897 (±0.0008172334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: NU-refinement map

Fileemd_34274_additional_1.map
AnnotationNU-refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 3DFlex half map

Fileemd_34274_half_map_1.map
Annotation3DFlex half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 3DFlex half map

Fileemd_34274_half_map_2.map
Annotation3DFlex half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Bre1-nucleosome complex

EntireName: Bre1-nucleosome complex
Components
  • Complex: Bre1-nucleosome complex
    • Complex: Histone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA
      • DNA: DNA (147-mer)
      • DNA: DNA (147-mer)
    • Complex: Bre1
      • Protein or peptide: E3 ubiquitin-protein ligase BRE1A
      • Protein or peptide: E3 ubiquitin-protein ligase BRE1B
  • Ligand: ZINC ION

+
Supramolecule #1: Bre1-nucleosome complex

SupramoleculeName: Bre1-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

+
Supramolecule #2: Histone

SupramoleculeName: Histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

+
Supramolecule #4: Bre1

SupramoleculeName: Bre1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

+
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: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

+
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: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

+
Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.990342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1

+
Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B type 1-J

+
Macromolecule #7: E3 ubiquitin-protein ligase BRE1A

MacromoleculeName: E3 ubiquitin-protein ligase BRE1A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.86182 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGIGNKRAA GEPGTSMPPE KKAAVEDSGT TVETIKLGGV SSTEELDIRT LQTKNRKLAE MLDQRQAIED ELREHIEKLE RRQATDDAS LLIVNRYWSQ FDENIRIILK RYDLEQGLGD LLTERKALVV PEPEPDSDSN QERKDDRERG EGQEPAFSFL A TLASSSSE ...String:
MSGIGNKRAA GEPGTSMPPE KKAAVEDSGT TVETIKLGGV SSTEELDIRT LQTKNRKLAE MLDQRQAIED ELREHIEKLE RRQATDDAS LLIVNRYWSQ FDENIRIILK RYDLEQGLGD LLTERKALVV PEPEPDSDSN QERKDDRERG EGQEPAFSFL A TLASSSSE EMESQLQERV ESSRRAVSQI VTVYDKLQEK VELLSRKLNS GDNLIVEEAV QELNSFLAQE NMRLQELTDL LQ EKHRTMS QEFSKLQSKV ETAESRVSVL ESMIDDLQWD IDKIRKREQR LNRHLAEVLE RVNSKGYKVY GAGSSLYGGT ITI NARKFE EMNAELEENK ELAQNRLCEL EKLRQDFEEV TTQNEKLKVE LRSAVEQVVK ETPEYRCMQS QFSVLYNESL QLKA HLDEA RTLLHGTRGT HQHQVELIER DEVSLHKKLR TEVIQLEDTL AQVRKEYEML RIEFEQTLAA NEQAGPINRE MRHLI SSLQ NHNHQLKGEV LRYKRKLREA QSDLNKTRLR SGSALLQSQS STEDPKDEPA ELKPDSEDLS SQSSASKASQ EDANEI KSK RDEEERERER REKERERERE REKEKERERE KQKLKESEKE RDSAKDKEKG KHDDGRKKEA EIIKQLKIEL KKAQESQ KE MKLLLDMYRS APKEQRDKVQ LMAAEKKSKA ELEDLRQRLK DLEDKEKKEN KKMADEDALR KIRAVEEQIE YLQKKLAM A KQEEEALLSE MDVTGQAFED MQEQNIRLMQ QLREKDDANF KLMSERIKSN QIHKLLKEEK EELADQVLTL KTQVDAQLQ VVRKLEEKEH LLQSNIGTGE KELGLRTQAL EMNKRKAMEA AQLADDLKAQ LELAQKKLHD FQDEIVENSV TKEKDMFNFK RAQEDISRL RRKLETTKKP DNVPKCDEIL MEEIKDYKAR LTCPCCNMRK KDAVLTKCFH VFCFECVKTR YDTRQRKCPK C NAAFGAND FHRIYIG

UniProtKB: E3 ubiquitin-protein ligase BRE1A

+
Macromolecule #8: E3 ubiquitin-protein ligase BRE1B

MacromoleculeName: E3 ubiquitin-protein ligase BRE1B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.863906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGPGNKRAA GDGGSGPPEK KLSREEKTTT TLIEPIRLGG ISSTEEMDLK VLQFKNKKLA ERLEQRQACE DELRERIEKL EKRQATDDA TLLIVNRYWA QLDETVEALL RCHESQGELS SAPEAPGTQE GPTCDGTPLP EPGTSELRDP LLMQLRPPLS E PALAFVVA ...String:
MSGPGNKRAA GDGGSGPPEK KLSREEKTTT TLIEPIRLGG ISSTEEMDLK VLQFKNKKLA ERLEQRQACE DELRERIEKL EKRQATDDA TLLIVNRYWA QLDETVEALL RCHESQGELS SAPEAPGTQE GPTCDGTPLP EPGTSELRDP LLMQLRPPLS E PALAFVVA LGASSSEEVE LELQGRMEFS KAAVSRVVEA SDRLQRRVEE LCQRVYSRGD SEPLSEAAQA HTRELGRENR RL QDLATQL QEKHHRISLE YSELQDKVTS AETKVLEMET TVEDLQWDIE KLRKREQKLN KHLAEALEQL NSGYYVSGSS SGF QGGQIT LSMQKFEMLN AELEENQELA NSRMAELEKL QAELQGAVRT NERLKVALRS LPEEVVRETG EYRMLQAQFS LLYN ESLQV KTQLDEARGL LLATKNSHLR HIEHMESDEL GLQKKLRTEV IQLEDTLAQV RKEYEMLRIE FEQNLAANEQ AGPIN REMR HLISSLQNHN HQLKGDAQRY KRKLREVQAE IGKLRAQASG SAHSTPNLGH PEDSGVSAPA PGKEEGGPGP VSTPDN RKE MAPVPGTTTT TTSVKKEELV PSEEDFQGIT PGAQGPSSRG REPEARPKRE LREREGPSLG PPPVASALSR ADREKAK VE ETKRKESELL KGLRAELKKA QESQKEMKLL LDMYKSAPKE QRDKVQLMAA ERKAKAEVDE LRSRIRELEE RDRRESKK I ADEDALRRIR QAEEQIEHLQ RKLGATKQEE EALLSEMDVT GQAFEDMQEQ NGRLLQQLRE KDDANFKLMS ERIKANQIH KLLREEKDEL GEQVLGLKSQ VDAQLLTVQK LEEKERALQG SLGGVEKELT LRSQALELNK RKAVEAAQLA EDLKVQLEHV QTRLREIQP CLAESRAARE KESFNLKRAQ EDISRLRRKL EKQRKVEVYA DADEILQEEI KEYKARLTCP CCNTRKKDAV L TKCFHVFC FECVRGRYEA RQRKCPKCNA AFGAHDFHRI YIS

UniProtKB: E3 ubiquitin-protein ligase BRE1B

+
Macromolecule #5: DNA (147-mer)

MacromoleculeName: DNA (147-mer) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.145754 KDa
SequenceString: (DC)(DT)(DG)(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:
(DC)(DT)(DG)(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)(DT)(DG)(DT)

+
Macromolecule #6: DNA (147-mer)

MacromoleculeName: DNA (147-mer) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (DA)(DC)(DA)(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)(DC)(DA)(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)(DC)(DA)(DG)

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83000

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more