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- EMDB-20767: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-20767
TitleStructural basis of COMPASS eCM recognition of the H2Bub nucleosome
Map dataCOMPASS eCM/H2Bub nucleosome
Sample
  • Complex: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
    • Complex: nucleosome
      • Protein or peptide: x 6 types
      • DNA: x 2 types
    • Complex: COMPASS eCM
      • Protein or peptide: x 6 types
    • Complex: ubiquitin
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development ...[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / 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 / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import
Similarity search - Function
: / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / Spp1/CFP1 / COMPASS (Complex proteins associated with Set1p) component N ...: / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / Spp1/CFP1 / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / : / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / 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 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Ubiquitin conserved site / Ubiquitin domain / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2B / Ubiquitin B / Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p / KLLA0E03521p ...Histone H2B / Ubiquitin B / Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p / KLLA0E03521p / KLLA0D07260p / KLLA0C10945p / KLLA0A08800p / Histone H3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHsu PL / Shi H / Zheng N
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol Cell / Year: 2019
Title: Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS.
Authors: Peter L Hsu / Hui Shi / Calvin Leonen / Jianming Kang / Champak Chatterjee / Ning Zheng /
Abstract: The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). ...The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that autoinhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By delineating the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
History
DepositionSep 26, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseNov 20, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uh5
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20767.png

Downloads & links

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Map

FileDownload / File: emd_20767.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOMPASS eCM/H2Bub nucleosome
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.015
Minimum - Maximum-0.045239784 - 0.099906646
Average (Standard dev.)0.00028896317 (±0.0024564413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 342.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0561.0561.056
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z342.144342.144342.144
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0450.1000.000

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Supplemental data

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Sample components

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Entire : Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

EntireName: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
Components
  • Complex: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
    • Complex: nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H2B
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
      • Protein or peptide: H3 N-terminus
    • Complex: COMPASS eCM
      • Protein or peptide: Swd3
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-4 specificHistone methyltransferase
      • Protein or peptide: Swd1
      • Protein or peptide: Spp1
      • Protein or peptide: Bre2
      • Protein or peptide: Sdc1
    • Complex: ubiquitin
      • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine

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Supramolecule #1: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

SupramoleculeName: Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #12
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: COMPASS eCM

SupramoleculeName: COMPASS eCM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#10, #13-#15
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: ubiquitin

SupramoleculeName: ubiquitin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #11
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 15.275879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CGIHAKRVTI MPKDIQLARR IRGERA

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

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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: 11.69465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVYL AAVLEYLTAE ILELAGNAAR DNKKTRIIPR HLQLAVRNDE ELNKLLGRV TIAQGGVLPN IQSVLLPK

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.82206 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT CYTSAK

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Macromolecule #8: Swd3

MacromoleculeName: Swd3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 36.458879 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MCDLDSVSDL TLTLRMLQFD KQVLPASGKI STSCQISPDG ELIAICQNTD MLVYEISSSK MMKLTTTHKE CINCLCWSPD SKCIASGSE DFTVEITHII YGRIRRLMGH TAPVISICYN NKGNILCSSS MDESIKEWHV LSGTALKTMS AHSDAVVSID I PKFDSSIL ...String:
MCDLDSVSDL TLTLRMLQFD KQVLPASGKI STSCQISPDG ELIAICQNTD MLVYEISSSK MMKLTTTHKE CINCLCWSPD SKCIASGSE DFTVEITHII YGRIRRLMGH TAPVISICYN NKGNILCSSS MDESIKEWHV LSGTALKTMS AHSDAVVSID I PKFDSSIL SSGSYDGLIR IFDTESGHCL KTLTYDKDWI AEDGVVPIST VKFSRNGKFL LVKSLDNVVK LWEYTRGTVV RT FLWPHQE TKAKLKYNCG LELIYPQGKD PLVISGNDSG SMCVWNVYSK NLVQKIDEKH RNSPLISISA SYDKVATLSL NGE CNLFRV H

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Macromolecule #9: Histone-lysine N-methyltransferase, H3 lysine-4 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-4 specific
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 31.448504 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: YQQIEQNGII RDNQIALNEK EFDSTLASTT GSFIAEGFKK IPDKLKSSYL LHHRRLAQPL NTVHNHQEQN FMALNGTEST NQEADLEQD NHNASSRLNR VFQRRFQQDI EAQRAAIGFE SDLLSLNQLT KRKKPVTFAR SAIHNWGLYA LEPIAAKEMI I EYVGESIR ...String:
YQQIEQNGII RDNQIALNEK EFDSTLASTT GSFIAEGFKK IPDKLKSSYL LHHRRLAQPL NTVHNHQEQN FMALNGTEST NQEADLEQD NHNASSRLNR VFQRRFQQDI EAQRAAIGFE SDLLSLNQLT KRKKPVTFAR SAIHNWGLYA LEPIAAKEMI I EYVGESIR QPVAEMREKR YIKSGIGSSY LFRIDENTVI DATKRGGIAR FINHCCEPSC TAKIIKVDGR KRIVIYALRD IG TNEELTY DYKFERETDE GERLPCLCGA PSCKGFLN

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Macromolecule #10: Swd1

MacromoleculeName: Swd1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 49.894656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MANLLLQDPF GVLKEYPEKL THTLEVPVAA VCVKFSPRGD YLAVGCSNGA IIIYDMDSLK PIAMLGTHSG AHTRSVQSVC WSNDGRYLW SSGRDWYAKL WDMTQPTKCF QQYKFDGPLW SCHVVRWNVC IVTVVEEPTA YVLTLTDRQN AFHCFPLLEQ D QDISGHGY ...String:
MANLLLQDPF GVLKEYPEKL THTLEVPVAA VCVKFSPRGD YLAVGCSNGA IIIYDMDSLK PIAMLGTHSG AHTRSVQSVC WSNDGRYLW SSGRDWYAKL WDMTQPTKCF QQYKFDGPLW SCHVVRWNVC IVTVVEEPTA YVLTLTDRQN AFHCFPLLEQ D QDISGHGY TLVACPHPTI ESIIITGTSK GWINAFQLDL ESGFEDKIRC CYEEKIANAN IKQIIISPSG TRIAINGSDR TI RQYQLIV EDNESEGGSS HSVSIELEHK YQDIINRLQW NTIFFSNHSG EYLVASAHGS SAHDLYLWET SSGSLVRVLE GAD EELLDI DWNFYSMRIA SNGFESGWVY MWSIVIPPKW SALAPDFEEV EENIDYQEKE NEFDIMDDDN NLQAMTEAEE IAID LCTPE KYDVRGNDIS MPSFVIPIDY EGVIIQQHWA HQEQ

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Macromolecule #11: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 11 / 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

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Macromolecule #12: H3 N-terminus

MacromoleculeName: H3 N-terminus / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 936.091 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTMQTAR

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Macromolecule #13: Spp1

MacromoleculeName: Spp1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 39.297867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLPSWCPRY DSRKHDPKTG EEVYCICKKP DTGELMVGCD GCDDWFHFSC LKIPEKYRDL VFSFYCSYCS AGITGPALIN GGKLPKTLW KRKCRLPECY TECDANSRSK YCSKKHAVQY VQSIVDKLNL PGVDKIALLR QLLNETTSLE EFKTLGRDKL P EVTSPLSK ...String:
MSLPSWCPRY DSRKHDPKTG EEVYCICKKP DTGELMVGCD GCDDWFHFSC LKIPEKYRDL VFSFYCSYCS AGITGPALIN GGKLPKTLW KRKCRLPECY TECDANSRSK YCSKKHAVQY VQSIVDKLNL PGVDKIALLR QLLNETTSLE EFKTLGRDKL P EVTSPLSK DQYSKLLEND QHLNKLINEH DELVSVKLSK LNEEDAVIEK YVNWIGEVNE RLSPHFNQPT GRKKSKSASK VT ICGYHNE FTIPRSVEEF LDKLLQLKED ENSNITSVDG VCVKTKCAKH QDWITLSQND LSEQKDSLEN VKRRLDLLIS VRT NQLRIS FFEQEMSNRV LPGVKT

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Macromolecule #14: Bre2

MacromoleculeName: Bre2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 47.286996 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSVPVIPYLD YDIVDLGSDI KKPDFPQLSE SHRINEQQYY ITEDTPLNKR NFMYQPCAAN LMLDKLKYCG TDYFDKSSIN LMDRSDKLA FSLDDHSVSV SENCGWRSVR SDVCMKEGKI YWEVEVKNVS DTSHIRCGIS RREASTETPV GCDFYGYSIR D KGLQVIHE ...String:
MSVPVIPYLD YDIVDLGSDI KKPDFPQLSE SHRINEQQYY ITEDTPLNKR NFMYQPCAAN LMLDKLKYCG TDYFDKSSIN LMDRSDKLA FSLDDHSVSV SENCGWRSVR SDVCMKEGKI YWEVEVKNVS DTSHIRCGIS RREASTETPV GCDFYGYSIR D KGLQVIHE GRLHTVLKPH EMQAGDRIGF LLTLPSLQSQ SEQAMDYSLK RIQELNNDDS RTNKRNKKFN KEFYKFLLRS CE PTNVVRD QIAIRYKNQL FYESTDYVKT TKPEYYDNRD DMQKFYELEN SSFEVFVNGV SHGIAFEGLT PFLPPFSELQ YNE KFYLHH WNKRNVTKGI EIRNKYVNNN RLGYYATLSS FQGGTASIIT EAMELKFLPK DVDIKTLNDI YNEQIASDIV WDLI DEIDT

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Macromolecule #15: Sdc1

MacromoleculeName: Sdc1 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Molecular weightTheoretical: 14.722625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSEPVMENMA PEDVVKLEKE EHIVPDIGVS SISTTEPLSP SGIPRESSGT VTSATAATTE REVSPKKELQ IDHDRVDPVA MIGGSTTRR YLNEHVTKHL LEGMKLIARE KPEDPLRVLG QFLIDASEMN QKPSS

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Macromolecule #6: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.825559 KDa
SequenceString: (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) ...String:
(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 #7: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.305852 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)

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #17: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 17 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 74.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215199

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