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- EMDB-26454: Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-26454
TitleComplex between MLL1-WRAD and an H2B-ubiquitinated nucleosome
Map data
Sample
  • Complex: MLL1 WRAD complex bound to the ubiquitinated nucleosome
    • Complex: MLL1 WRAD complex
      • Protein or peptide: x 6 types
    • Complex: nucleosome
      • Protein or peptide: x 4 types
    • DNA: x 2 types
  • Ligand: x 2 types
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / endosomal transport / histone methyltransferase complex / regulation of tubulin deacetylation ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / endosomal transport / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / hemopoiesis / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / trans-Golgi network / mitotic spindle / PKMTs methylate histone lysines / beta-catenin binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / modification-dependent protein catabolic process / response to estrogen / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly / Neddylation / HATs acetylate histones / histone binding / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / protein heterodimerization activity / ubiquitin protein ligase binding / DNA damage response / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / : ...: / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / : / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SPRY domain / 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 / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / Ubiquitin-like 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 H3 / cDNA FLJ56846, highly similar to Zinc finger protein HRX / Ubiquitin B / Histone H2B 1.1 / WD repeat-containing protein 5 / Histone H4 / Retinoblastoma-binding protein 5 / Histone H2A / Protein dpy-30 homolog / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsNiklas HA / Rahman S / Worden EJ / Wolberger C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM130393 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome.
Authors: Sanim Rahman / Niklas A Hoffmann / Evan J Worden / Marissa L Smith / Kevin E W Namitz / Bruce A Knutson / Michael S Cosgrove / Cynthia Wolberger /
Abstract: The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core ...The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, DR5, bBp5, sh2L, and PY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
History
DepositionMar 18, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26454.png

Downloads & links

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Map

FileDownload / File: emd_26454.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 0.00732
Minimum - Maximum-0.0359005 - 0.0534346
Average (Standard dev.)0.00016733108 (±0.0016520167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26454_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_26454_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_26454_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_26454_half_map_2.map
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Sample components

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Entire : MLL1 WRAD complex bound to the ubiquitinated nucleosome

EntireName: MLL1 WRAD complex bound to the ubiquitinated nucleosome
Components
  • Complex: MLL1 WRAD complex bound to the ubiquitinated nucleosome
    • Complex: MLL1 WRAD complex
      • Protein or peptide: cDNA FLJ56846, highly similar to Zinc finger protein HRX
      • Protein or peptide: WD repeat-containing protein 5
      • Protein or peptide: Set1/Ash2 histone methyltransferase complex subunit ASH2
      • Protein or peptide: Retinoblastoma-binding protein 5
      • Protein or peptide: Polyubiquitin-B
      • Protein or peptide: Protein dpy-30 homolog
    • Complex: nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • DNA: 601 DNA (146-MER)
    • DNA: 601 DNA (146-MER)
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

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Supramolecule #1: MLL1 WRAD complex bound to the ubiquitinated nucleosome

SupramoleculeName: MLL1 WRAD complex bound to the ubiquitinated nucleosome
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#12

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Supramolecule #2: MLL1 WRAD complex

SupramoleculeName: MLL1 WRAD complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7-#12
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)
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: 15.383028 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MART(NLE)QTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIA QDF KTDLRFQSSA V(NLE)ALQEASEA YLVALFEDTN LCAIHAKRVT I(NLE)PKDIQLAR RIRGERA

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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

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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

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.629911 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTCY TSAK

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Macromolecule #7: cDNA FLJ56846, highly similar to Zinc finger protein HRX

MacromoleculeName: cDNA FLJ56846, highly similar to Zinc finger protein HRX
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.247025 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFRFHKPEEA NEPPLNPHGS ARAEVHLRKS AFDMFNFLAS KHRQPPEYNP NDEEEEEVQL KSARRATSMD LPMPMRFRHL KKTSKEAVG VYRSPIHGRG LFCKRNIDAG EMVIEYAGNV IRSIQTDKRE KYYDSKGIGC YMFRIDDSEV VDATMHGNAA R FINHSCEP ...String:
MFRFHKPEEA NEPPLNPHGS ARAEVHLRKS AFDMFNFLAS KHRQPPEYNP NDEEEEEVQL KSARRATSMD LPMPMRFRHL KKTSKEAVG VYRSPIHGRG LFCKRNIDAG EMVIEYAGNV IRSIQTDKRE KYYDSKGIGC YMFRIDDSEV VDATMHGNAA R FINHSCEP NCYSRVINID GQKHIVIFAM RKIYRGEELT YDYKFPIEDA SNKLPCNCGA KKCRKFLN

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Macromolecule #8: WD repeat-containing protein 5

MacromoleculeName: WD repeat-containing protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.648371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSATEEKKPE TEAARAQPTP SSSATQSKPT PVKPNYALKF TLAGHTKAVS SVKFSPNGEW LASSSADKLI KIWGAYDGKF EKTISGHKL GISDVAWSSD SNLLVSASDD KTLKIWDVSS GKCLKTLKGH SNYVFCCNFN PQSNLIVSGS FDESVRIWDV K TGKCLKTL ...String:
GSATEEKKPE TEAARAQPTP SSSATQSKPT PVKPNYALKF TLAGHTKAVS SVKFSPNGEW LASSSADKLI KIWGAYDGKF EKTISGHKL GISDVAWSSD SNLLVSASDD KTLKIWDVSS GKCLKTLKGH SNYVFCCNFN PQSNLIVSGS FDESVRIWDV K TGKCLKTL PAHSDPVSAV HFNRDGSLIV SSSYDGLCRI WDTASGQCLK TLIDDDNPPV SFVKFSPNGK YILAATLDNT LK LWDYSKG KCLKTYTGHK NEKYCIFANF SVTGGKWIVS GSEDNLVYIW NLQTKEIVQK LQGHTDVVIS TACHPTENII ASA ALENDK TIKLWKSDC

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Macromolecule #9: Set1/Ash2 histone methyltransferase complex subunit ASH2

MacromoleculeName: Set1/Ash2 histone methyltransferase complex subunit ASH2
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.288758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTQAGSVDE ENGRQLGEVE LQCGICTKWF TADTFGIDTS SCLPFMTNYS FHCNVCHHSG NTYFLRKQAN LKEMCLSALA NLTWQSRTQ DEHPKTMFSK DKDIIPFIDK YWECMTTRQR PGKMTWPNNI VKTMSKERDV FLVKEHPDPG SKDPEEDYPK F GLLDQDLS ...String:
MDTQAGSVDE ENGRQLGEVE LQCGICTKWF TADTFGIDTS SCLPFMTNYS FHCNVCHHSG NTYFLRKQAN LKEMCLSALA NLTWQSRTQ DEHPKTMFSK DKDIIPFIDK YWECMTTRQR PGKMTWPNNI VKTMSKERDV FLVKEHPDPG SKDPEEDYPK F GLLDQDLS NIGPAYDNQK QSSAVSTSGN LNGGIAAGSS GKGRGAKRKQ QDGGTTGTTK KARSDPLFSA QRLPPHGYPL EH PFNKDGY RYILAEPDPH APDPEKLELD CWAGKPIPGD LYRACLYERV LLALHDRAPQ LKISDDRLTV VGEKGYSMVR ASH GVRKGA WYFEITVDEM PPDTAARLGW SQPLGNLQAP LGYDKFSYSW RSKKGTKFHQ SIGKHYSSGY GQGDVLGFYI NLPE DTETA KSLPDTYKDK ALIKFKSYLY FEEKDFVDKA EKSLKQTPHS EIIFYKNGVN QGVAYKDIFE GVYFPAISLY KSCTV SINF GPCFKYPPKD LTYRPMSDMG WGAVVEHTLA DVLYHVETEV DGRRSPPWEP

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Macromolecule #10: Retinoblastoma-binding protein 5

MacromoleculeName: Retinoblastoma-binding protein 5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.223477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLELLESFG QNYPEEADGT LDCISMALTC TFNRWGTLLA VGCNDGRIVI WDFLTRGIAK IISAHIHPVC SLCWSRDGHK LVSASTDNI VSQWDVLSGD CDQRFRFPSP ILKVQYHPRD QNKVLVCPMK SAPVMLTLSD SKHVVLPVDD DSDLNVVASF D RRGEYIYT ...String:
MNLELLESFG QNYPEEADGT LDCISMALTC TFNRWGTLLA VGCNDGRIVI WDFLTRGIAK IISAHIHPVC SLCWSRDGHK LVSASTDNI VSQWDVLSGD CDQRFRFPSP ILKVQYHPRD QNKVLVCPMK SAPVMLTLSD SKHVVLPVDD DSDLNVVASF D RRGEYIYT GNAKGKILVL KTDSQDLVAS FRVTTGTSNT TAIKSIEFAR KGSCFLINTA DRIIRVYDGR EILTCGRDGE PE PMQKLQD LVNRTPWKKC CFSGDGEYIV AGSARQHALY IWEKSIGNLV KILHGTRGEL LLDVAWHPVR PIIASISSGV VSI WAQNQV ENWSAFAPDF KELDENVEYE ERESEFDIED EDKSEPEQTG ADAAEDEEVD VTSVDPIAAF CSSDEELEDS KALL YLPIA PEVEDPEENP YGPPPDAVQT SLMDEGASSE KKRQSSADGS QPPKKKPKTT NIELQGVPND EVHPLLGVKG DGKSK KKQA GRPKGSKGKE KDSPFKPKLY KGDRGLPLEG SAKGKVQAEL SQPLTAGGAI SELL

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Macromolecule #11: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.164521 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QGSHMMQIFV KTLTGKTITL EVEPSDTIEN VKAKIQDKEG IPPDQQRLIF AGKQLEDGRT LSDYNIQKES TLHLVLRLRG C

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Macromolecule #12: Protein dpy-30 homolog

MacromoleculeName: Protein dpy-30 homolog / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.733196 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMDPMEPEQ MLEGQTQVAE NPHSEYGLTD NVERIVENEK INAEKSSKQK VDLQSLPTRA YLDQTVVPIL LQGLAVLAKE RPPNPIEFL ASYLLKNKAQ FEDRN

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Macromolecule #5: 601 DNA (146-MER)

MacromoleculeName: 601 DNA (146-MER) / type: dna / ID: 5 / 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 #6: 601 DNA (146-MER)

MacromoleculeName: 601 DNA (146-MER) / type: dna / ID: 6 / 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 #13: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 13 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5091 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8140


Details: rescaled and lowpass filtered to 60A
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66449
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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