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- EMDB-20765: Structural basis of COMPASS eCM recognition of an unmodified nucl... -

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Basic information

Entry
Database: EMDB / ID: EMD-20765
TitleStructural basis of COMPASS eCM recognition of an unmodified nucleosome
Map dataCOMPASS eCM/unmodified ribosome
Sample
  • Complex: Yeast COMPASS eCM bound to an unmodified nucleosome
    • Complex: nucleosome
      • Protein or peptide: x 6 types
      • DNA: x 2 types
    • Complex: COMPASS eCM
      • Protein or peptide: x 6 types
  • Ligand: x 2 types
KeywordsComplex / methyltransferase / epigenetics / chromatin / nucleosome / TRANSFERASE-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / : / structural constituent of chromatin / nucleosome / chromosome / methylation / histone binding / transcription cis-regulatory region binding ...[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / : / structural constituent of chromatin / nucleosome / chromosome / methylation / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / positive regulation of DNA-templated transcription / DNA binding / RNA binding / nucleus / metal ion binding
Similarity search - Function
Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N ...Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Spp1/CFP1 / : / 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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / : / Zinc finger PHD-type profile. / 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 H2A / Histone 2A / 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 / Zinc finger, PHD-finger / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2B / Histone H2B 1.1 / Histone H4 / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHsu PL / Shi H
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-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ugm
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20765.png

Downloads & links

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Map

FileDownload / File: emd_20765.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOMPASS eCM/unmodified ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 342.144 Å		1.06 Å/pix.
x 324 pix.
= 342.144 Å		1.06 Å/pix.
x 324 pix.
= 342.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.012
Minimum - Maximum-0.06289047 - 0.11903959
Average (Standard dev.)0.00020239587 (±0.0021785435)
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-0.0630.1190.000

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Supplemental data

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Sample components

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Entire : Yeast COMPASS eCM bound to an unmodified nucleosome

EntireName: Yeast COMPASS eCM bound to an unmodified nucleosome
Components
  • Complex: Yeast COMPASS eCM bound to an unmodified 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 1.1
      • 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 specific
      • Protein or peptide: Swd1
      • Protein or peptide: Spp1
      • Protein or peptide: Bre2
      • Protein or peptide: Sdc1
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ZINC ION

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Supramolecule #1: Yeast COMPASS eCM bound to an unmodified nucleosome

SupramoleculeName: Yeast COMPASS eCM bound to an unmodified nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #11
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: COMPASS eCM

SupramoleculeName: COMPASS eCM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#10, #12-#14
Source (natural)Organism: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)

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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

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

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

UniProtKB: Histone H2A

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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

UniProtKB: Histone H2B

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Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.83407 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KSRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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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

UniProtKB: KLLA0E24487p

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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

UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-4 specific

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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

UniProtKB: KLLA0A08800p

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Macromolecule #11: H3 N-terminus

MacromoleculeName: H3 N-terminus / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 378.444 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TMQ

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Macromolecule #12: Spp1

MacromoleculeName: Spp1 / type: protein_or_peptide / ID: 12 / 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

UniProtKB: KLLA0D07260p

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Macromolecule #13: Bre2

MacromoleculeName: Bre2 / 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: 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

UniProtKB: KLLA0C10945p

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Macromolecule #14: Sdc1

MacromoleculeName: Sdc1 / type: protein_or_peptide / ID: 14 / 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

UniProtKB: KLLA0E03521p

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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: 45.114746 KDa
SequenceString: (DC)(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:
(DC)(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 #15: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 15 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100905
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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