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- EMDB-64885: Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to t... -

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Basic information

Entry
Database: EMDB / ID: EMD-64885
TitleCryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Map dataCryo-EM density map of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Sample
  • Complex: ncPRC1.1 E3 : E2~ub complex
    • Protein or peptide: x 9 types
    • DNA: x 2 types
  • Ligand: x 1 types
Keywordsnucleosome modification / transcriptional regulation / GENE REGULATION
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / Signaling by BMP / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / Signaling by BMP / PcG protein complex / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / protein K11-linked ubiquitination / protein K6-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / anterior/posterior axis specification / female meiosis I / positive regulation of protein monoubiquitination / : / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / seminiferous tubule development / Formation of the ternary complex, and subsequently, the 43S complex / female gonad development / Transcriptional Regulation by E2F6 / Ribosomal scanning and start codon recognition / germ cell development / Translation initiation complex formation / ubiquitin conjugating enzyme activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / MLL1 complex / male meiosis I / SARS-CoV-1 modulates host translation machinery / : / Peptide chain elongation / negative regulation of BMP signaling pathway / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / protein monoubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ubiquitin ligase complex / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SUMOylation of DNA damage response and repair proteins / protein autoubiquitination / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / neuron projection morphogenesis / protein K48-linked ubiquitination / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / SUMOylation of transcription cofactors / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / epigenetic regulation of gene expression / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / cytosolic ribosome / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / regulation of neuron apoptotic process / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / protein modification process / VLDLR internalisation and degradation
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ring finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2B / Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 D3 / Histone H4 / Ubiquitin-ribosomal protein eS31 fusion protein / Histone H2A / E3 ubiquitin-protein ligase RING2 / Polycomb group RING finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYu Y / Cai D / Zhang YZ / Huang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural mechanisms of PRC1-mediated interplay between gene repression and activation
Authors: Yu Y / Cai D / Zhang YZ / Huang J
History
DepositionJun 2, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64885.png

Downloads & links

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Map

FileDownload / File: emd_64885.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.04277499 - 0.09608101
Average (Standard dev.)-0.00005686025 (±0.0036945057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64885_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM density map of the cPRC1-UbcH5c E3-E2 complex...

Fileemd_64885_additional_1.map
AnnotationCryo-EM density map of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome with mask on H2AK119ub
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map 2 of the cPRC1-UbcH5c E3-E2 complex...

Fileemd_64885_half_map_1.map
AnnotationEM half map_2 of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map 1 of the cPRC1-UbcH5c E3-E2 complex...

Fileemd_64885_half_map_2.map
AnnotationEM half map_1 of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ncPRC1.1 E3 : E2~ub complex

EntireName: ncPRC1.1 E3 : E2~ub complex
Components
  • Complex: ncPRC1.1 E3 : E2~ub complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (144-MER)
    • DNA: DNA (145-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Polycomb group RING finger protein 1
  • Ligand: ZINC ION

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Supramolecule #1: ncPRC1.1 E3 : E2~ub complex

SupramoleculeName: ncPRC1.1 E3 : E2~ub complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Details: The ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.91319 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TCYTSAK

UniProtKB: Histone H2B

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Macromolecule #7: E3 ubiquitin-protein ligase RING2

MacromoleculeName: E3 ubiquitin-protein ligase RING2 / 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: 37.706371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQAVQTNGT QPLSKTWELS LYELQRTPQE AITDGLEIVV SPRSLHSELM CPICLDMLKN TMTTKECLHR FCADCIITAL RSGNKECPT CRKKLVSKRS LRPDPNFDAL ISKIYPSRDE YEAHQERVLA RINKHNNQQA LSHSIEEGLK IQAMNRLQRG K KQQIENGS ...String:
MSQAVQTNGT QPLSKTWELS LYELQRTPQE AITDGLEIVV SPRSLHSELM CPICLDMLKN TMTTKECLHR FCADCIITAL RSGNKECPT CRKKLVSKRS LRPDPNFDAL ISKIYPSRDE YEAHQERVLA RINKHNNQQA LSHSIEEGLK IQAMNRLQRG K KQQIENGS GAEDNGDSSH CSNASTHSNQ EAGPSNKRTK TSDDSGLELD NNNAAMAIDP VMDGASEIEL VFRPHPTLME KD DSAQTRY IKTSGNATVD HLSKYLAVRL ALEELRSKGE SNQMNLDTAS EKQYTIYIAT ASGQFTVLNG SFSLELVSEK YWK VNKPME LYYAPTKEHK

UniProtKB: E3 ubiquitin-protein ligase RING2

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Macromolecule #8: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.760184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRINKEL SDLARDPPAQ CRAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSISLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

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Macromolecule #9: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.622922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

UniProtKB: Polyubiquitin-B

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Macromolecule #10: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #11: Polycomb group RING finger protein 1

MacromoleculeName: Polycomb group RING finger protein 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.394438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASPQGGQIA IAMRLRNQLQ SVYKMDPLRN EEEVRVKIKD LNEHIVCCLC AGYFVDATTI TECLHTFCKS CIVKYLQTSK YCPMCNIKI HETQPLLNLK LDRVMQDIVY KLVPGLQDSE EKRIREFYQS RGLDRVTQPT GEEPALSNLG LPFSSFDHSK A HYYRYDEQ ...String:
MASPQGGQIA IAMRLRNQLQ SVYKMDPLRN EEEVRVKIKD LNEHIVCCLC AGYFVDATTI TECLHTFCKS CIVKYLQTSK YCPMCNIKI HETQPLLNLK LDRVMQDIVY KLVPGLQDSE EKRIREFYQS RGLDRVTQPT GEEPALSNLG LPFSSFDHSK A HYYRYDEQ LNLCLERLSS GKDKNKSVLQ NKYVRCSVRA EVRHLRRVLC HRLMLNPQHV QLLFDNEVLP DHMTMKQIWL SR WFGKPSP LLLQYSVKEK RR

UniProtKB: Polycomb group RING finger protein 1

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Macromolecule #5: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.217172 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #6: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.992648 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45415
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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