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- EMDB-51643: State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-51643
TitleState 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome
Map data
Sample
  • Complex: State 2 SETD2 bound to proximal H3 tail
    • DNA: Non-Template DNA
    • Protein or peptide: Histone-lysine N-methyltransferase SETD2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: FACT complex subunit SPT16
  • DNA: Template DNA
KeywordsRNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 / TRANSCRIPTION
Function / homology
Function and homology information


peptidyl-lysine trimethylation / FACT complex / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon ...peptidyl-lysine trimethylation / FACT complex / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / positive regulation of ossification / regulation of protein localization to chromatin / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / positive regulation of interferon-alpha production / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / alpha-tubulin binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / nucleosome binding / Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Replacement of protamines by nucleosomes in the male pronucleus / Formation of RNA Pol II elongation complex / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / RNA Polymerase II Pre-transcription Events / positive regulation of autophagy / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of cytokinesis / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / stem cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / HATs acetylate histones
Similarity search - Function
FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 ...FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Creatinase/Aminopeptidase P/Spt16, N-terminal / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / TFIIS/LEDGF domain superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / WW domain / WW/rsp5/WWP domain signature. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / SET domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / SET domain profile. / SET domain / WW domain / : / 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 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
Histone H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase SETD2 / FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.84 Å
AuthorsWalshe JL / Ochmann M / Dienemann C / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanism of co-transcriptional H3K36 methylation by SETD2.
Authors: James L Walshe / Moritz Ochmann / Ute Neef / Olexandr Dybkov / Christian Dienemann / Christiane Oberthür / Aiturgan Zheenbekova / Henning Urlaub / Patrick Cramer /
Abstract: H3K36me3 is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase ...H3K36me3 is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase SETD2 associates with RNA polymerase II. Here we present three cryo-EM structures of SETD2 bound to RNA polymerase II elongation complexes at different states of nucleosome passage. Together with functional probing, our results suggest a 3-step mechanism of transcription-coupled H3K36me3 deposition. First, binding to the elongation factor SPT6 tethers the catalytic SET domain in proximity to the upstream DNA. Second, RNA polymerase II nucleosome passage leads to the transfer of a hexasome from downstream to upstream, poised for methylation. Finally, continued transcription leads to upstream nucleosome reassembly, partial dissociation of the histone chaperone FACT and sequential methylation of both H3 tails, completing H3K36me3 deposition of an upstream nucleosome after RNA polymerase II passage.
History
DepositionSep 26, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51643.png

Downloads & links

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Map

FileDownload / File: emd_51643.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.049310893 - 0.0731376
Average (Standard dev.)0.000108972854 (±0.0016883784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51643_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51643_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : State 2 SETD2 bound to proximal H3 tail

EntireName: State 2 SETD2 bound to proximal H3 tail
Components
  • Complex: State 2 SETD2 bound to proximal H3 tail
    • DNA: Non-Template DNA
    • Protein or peptide: Histone-lysine N-methyltransferase SETD2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: FACT complex subunit SPT16
  • DNA: Template DNA

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Supramolecule #1: State 2 SETD2 bound to proximal H3 tail

SupramoleculeName: State 2 SETD2 bound to proximal H3 tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Non-Template DNA

MacromoleculeName: Non-Template DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.47093 KDa
SequenceString: (DA)(DT)(DC)(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:
(DA)(DT)(DC)(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) (DA)(DT)(DC)(DA)(DC)(DT) (DG)(DT)(DC) (DG)(DC)(DG)(DG)(DC)(DC)(DC)(DT)(DT)(DG) (DT)(DG)(DT)(DT)(DC)(DA)(DG) (DG)(DA) (DG)(DC)(DC)(DA)(DG)(DC)(DA)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DG)(DG)(DG)(DA) (DG) (DC)

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Macromolecule #3: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 55.939559 KDa
SequenceString: (DG)(DC)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DG)(DC) (DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DC) (DG) (DA)(DC)(DA)(DG)(DT)(DG) ...String:
(DG)(DC)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DG)(DC) (DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DT)(DG)(DC)(DC)(DG)(DC) (DG) (DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (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)(DG) (DA) (DT)

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Macromolecule #2: Histone-lysine N-methyltransferase SETD2

MacromoleculeName: Histone-lysine N-methyltransferase SETD2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine36 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.887328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAETSVPPG SALVGPSCVM DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDC LNRLLMIECS SRCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK A RVKEYARN ...String:
SNAETSVPPG SALVGPSCVM DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDC LNRLLMIECS SRCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK A RVKEYARN KNIHYYFMAL KNDEIIDATQ KGNCSRFMNH SCEPNCETQK WTVNGQLRVG FFTTKLVPSG SELTFDYQFQ RY GKEAQKC FCGSANCRGY LGGENRVSIR AAGGKMKKER SRKKDSVDGE LEALMENGEG LSDKNQVLSL SRLMVRIETL EQK LTCLEL IQNTHSQSCL KSFLERHGLS LLWIWMAELG DGRESNQKLQ EEIIKTLEHL PIPTKNMLEE SKVLPIIQRW SQTK TAVPP LSEGDGYSSE NTSRAHTPLN TPDPSTKLST EADTDTPKKL MFRRLKIISE NSMDSAISDA TSELEGKDGK EDLDQ LENV PVEEEEELQS QQLLPQQLPE CKVDSETNIE ASKLPTSEPE ADAEIELKES NGTKLEEPIN EETPSQDEEE GVSDVE SER SQEQPDKTVD ISDLATKLLD SWKDLKEVYR IPKKSQTEKE NTTTERGRDA VGFRDQTPAP KTPNRSRERD PDKQTQN KE KRKRRSSLSP PSSAYERGTK RPDDRYDTPT SKKKVRIKDR NKLSTEERRK LFEQEVAQRE AQKQQQQMQN LGMTSPLP Y DSLGYNAPHH PFAGYPPGYP MQAYVDPSNP NAGKVLLPTP SMDPVCSPAP YDHAQPLVGH STEPLSAPPP VPVVPHVAA PVEVSSSQYV AQSDGVVHQD SSVAVLPVPA PGPVQGQNYS VWDSNQQSVS VQQQYSPAQS QATIYYQGQT CPTVYGVTSP YSQTTPPIV QSYAQPSLQY IQGQQIFTAH PQGVVVQPAA AVTTIVAPGQ PQPLQPSEMV VTNNLLDLPP PSPPKPKTIV L PPNWKTAR DPEGKIYYYH VITRQTQWDP PTWESPGDDA SLEHEAEMDL GTPTYDENPM KASKKPKTAE ADTSSELAKK SK EVFRKEM SQFIVQCLNP YRKPDCKVGR ITTTEDFKHL ARKLTHGVMN KELKYCKNPE DLECNENVKH KTKEYIKKYM QKF GAVYKP KEDTELE

UniProtKB: Histone-lysine N-methyltransferase SETD2

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Macromolecule #4: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.391052 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVMKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #6: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.721133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAPWMSGRG KQGGKARAKA KTRSSRAGLQ FPVGRVHRLL RKGNYSERVG AGAPVYLAAV LEYLTAEILE LAGNAARDNK KTRIIPRHL QLAIRNDEEL NKLLGRVTIA QGGVLPNIQA VLLPKKTESH HKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #7: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.921213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #8: FACT complex subunit SPT16

MacromoleculeName: FACT complex subunit SPT16 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.290961 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNMAVTLDKD AYYRRVKRLY SNWRKGEDEY ANVDAIVVSV GVDEEIVYAK STALQTWLFG YELTDTIMVF CDDKIIFMAS KKKVEFLKQ IANTKGNENA NGAPAITLLI REKNESNKSS FDKMIEAIKE SKNGKKIGVF SKDKFPGEFM KSWNDCLNKE G FDKIDISA ...String:
SNMAVTLDKD AYYRRVKRLY SNWRKGEDEY ANVDAIVVSV GVDEEIVYAK STALQTWLFG YELTDTIMVF CDDKIIFMAS KKKVEFLKQ IANTKGNENA NGAPAITLLI REKNESNKSS FDKMIEAIKE SKNGKKIGVF SKDKFPGEFM KSWNDCLNKE G FDKIDISA VVAYTIAVKE DGELNLMKKA ASITSEVFNK FFKERVMEIV DADEKVRHSK LAESVEKAIE EKKYLAGADP ST VEMCYPP IIQSGGNYNL KFSVVSDKNH MHFGAITCAM GIRFKSYCSN LVRTLMVDPS QEVQENYNFL LQLQEELLKE LRH GVKICD VYNAVMDVVK KQKPELLNKI TKNLGFGMGI EFREGSLVIN SKNQYKLKKG MVFSINLGFS DLTNKEGKKP EEKT YALFI GDTVLVDEDG PATVLTSVKK KVKNVGIFLK NEDEEEEEEE KDEAEDLLGR GSRAALLTER TRNEMTAEEK RRAHQ KELA AQLNEEAKRR LTEQKGEQQI QKARKSNVSY KNPSLMPKEP HIREMKIYID KKYETVIMPV FGIATPFHIA TIKNIS MSV EGDYTYLRIN FYCPGSALGR NEGNIFPNPE ATFVKEITYR ASNIKAPGEQ TVPALNLQNA FRIIKEVQKR YKTREAE EK EKEGIVKQDS LVINLNRSNP KLKDLYIRPN IAQKRMQGSL EAHVNGFRFT SVRGDKVDIL YNNIKHALFQ PCDGEMII V LHFHLKNAIM FGKKRHTDVQ FYTEVGEITT DLGKHQHMHD RDDLYAEQME REMRHKLKTA FKNFIEKVEA LTKEELEFE VPFRDLGFNG APYRSTCLLQ PTSSALVNAT EWPPFVVTLD EVELIHFERV QFHLKNFDMV IVYKDYSKKV TMINAIPVAS LDPIKEWLN SCDLKYTEGV QSLNWTKIMK TIVDDPEGFF EQGGWSFLEP EGEGSDAEEG DSESEIEDET FNPSEDDYEE E EEDSDEDY SSEAEESDYS KESLGSEEES GKDWDELEEE ARKADRESRY EEEEEQSRSM SRKRKASVHS SGRGSNRGSR HS SAPPKKK RK

UniProtKB: FACT complex subunit SPT16

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 80067
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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  • 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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