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- EMDB-48626: Structure of a native Drosophila melanogaster Nucleosome Elongati... -

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Basic information

Entry
Database: EMDB / ID: EMD-48626
TitleStructure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
Map dataComposite map of the locally refined Pol II and nucleosome from the Nucleosome Elongation Complex.
Sample
  • Complex: Native purified Nucleosome Elongation Complex from Drosophila melanogaster
    • RNA: x 1 types
    • DNA: x 2 types
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
Keywordspolymerase / Pol II / transcription / mRNA
Function / homology
Function and homology information


Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation ...Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Processing of Capped Intron-Containing Pre-mRNA / Dual incision in TC-NER / polytene chromosome puff / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / nucleosomal DNA binding / nuclear chromosome / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromatin organization / chromosome / cellular response to heat / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / protein heterodimerization activity / protein-containing complex binding / chromatin / nucleolus / DNA binding / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. ...RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits 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 / 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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
GH07456p / Histone H2B / Histone H3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Histone H2A / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / GEO11084p1 ...GH07456p / Histone H2B / Histone H3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Histone H2A / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / GEO11084p1 / RPB5 homolog / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsVenette-Smith NL / Vishwakarma RK / Dollinger R / Schultz J / Venkatakrishnan V / Babitzke P / Anand G / Gilmour DS / Armache J-P / Murakami K
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047477 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098399 United States
CitationJournal: To Be Published
Title: Structural Characterization of Native RNA Polymerase II Transcription Complexes in Drosophila melanogaster
Authors: Venette-Smith NL / Vishwakarma RK / Dollinger R / Schultz J / Venkatakrishnan V / Babitzke P / Anand G / Gilmour DS / Armache J-P / Murakami K
History
DepositionJan 13, 2025-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48626.png

Downloads & links

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Map

FileDownload / File: emd_48626.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the locally refined Pol II and nucleosome from the Nucleosome Elongation Complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.15 Å/pix.
x 360 pix.
= 415.368 Å		1.15 Å/pix.
x 360 pix.
= 415.368 Å		1.15 Å/pix.
x 360 pix.
= 415.368 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1538 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.13090104 - 0.5718973
Average (Standard dev.)0.001082451 (±0.024066893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 415.368 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite map of the locally refined and auto-sharpened...

Fileemd_48626_additional_1.map
AnnotationComposite map of the locally refined and auto-sharpened Pol II and nucleosome from the Nucleosome Elongation Complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native purified Nucleosome Elongation Complex from Drosophila mel...

EntireName: Native purified Nucleosome Elongation Complex from Drosophila melanogaster
Components
  • Complex: Native purified Nucleosome Elongation Complex from Drosophila melanogaster
    • RNA: RNA
    • DNA: Template DNA
    • DNA: Non-template DNA
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB12
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB5
  • Ligand: ZINC ION

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Supramolecule #1: Native purified Nucleosome Elongation Complex from Drosophila mel...

SupramoleculeName: Native purified Nucleosome Elongation Complex from Drosophila melanogaster
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Details: A composite structure of a native purified Nucleosome Elongation Complex (Pol II EC - nucleosome)
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: RNA

MacromoleculeName: RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 3.2471 KDa
SequenceString:
AAAAAAAAAA

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Macromolecule #2: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 53.243816 KDa
SequenceString: (DA)(DT)(DC)(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:
(DA)(DT)(DC)(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)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DC)(DC)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

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Macromolecule #3: Non-template DNA

MacromoleculeName: Non-template DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 50.692539 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DC)(DA)(DC) (DG) (DT)(DG)(DC)(DC)(DT)(DG) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(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) (DG)(DA) (DT)

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.552494 KDa
SequenceString:
AKSRSNRAGL QFPVGRIHRL LRKGNYAERV GAGAPVYLAA VMEYLAAEVL ELAGNAARDN KKTRIIPRHL QLAIRNDEEL NKLLSGVTI AQGGVLPNIQ AVLLPKK

UniProtKB: Histone H2A

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 10.979741 KDa
SequenceString:
KKRKRKESYA IYIYKVLKQV HPDTGISSKA MSIMNSFVND IFERIAAEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKA VTKYTSSK

UniProtKB: Histone H2B

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Macromolecule #6: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.74677 KDa
SequenceString:
KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRFQ SSAVMALQEA SEAYLVGLFE DTNLCAIHAK RVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3

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Macromolecule #7: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 9.067586 KDa
SequenceString:
RDNIQGITKP AIRRLARRGG VKRISGLIYE ETRGVLKVFL ENVIRDAVTY TEHAKRKTVT AMDVVYALKR QGRTLYGFGG

UniProtKB: Histone H4

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Macromolecule #8: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 166.420375 KDa
SequenceString: SKAPLRQVKR VQFGILSPDE IRRMSVTEGG VQFAETMEGG RPKLGGLMDP RQGVIDRTSR CQTCAGNMTE CPGHFGHIDL AKPVFHIGF ITKTIKILRC VCFYCSKMLV SPHNPKIKEI VMKSRGQPRK RLAYVYDLCK GKTICEGGED MDLTKENQQP D PNKKPGHG ...String:
SKAPLRQVKR VQFGILSPDE IRRMSVTEGG VQFAETMEGG RPKLGGLMDP RQGVIDRTSR CQTCAGNMTE CPGHFGHIDL AKPVFHIGF ITKTIKILRC VCFYCSKMLV SPHNPKIKEI VMKSRGQPRK RLAYVYDLCK GKTICEGGED MDLTKENQQP D PNKKPGHG GCGHYQPSIR RTGLDLTAEW KHQNEDSQEK KIVVSAERVW EILKHITDEE CFILGMDPKY ARPDWMIVTV LP VPPLAVR PAVVMFGAAK NQDDLTHKLS DIIKANNELR KNEASGAAAH VIQENIKMLQ FHVATLVDND MPGMPRAMQK SGK PLKAIK ARLKGKEGRI RGNLMGKRVD FSARTVITPD PNLRIDQVGV PRSIAQNLTF PELVTPFNID RMQELVRRGN SQYP GAKYI VRDNGERIDL RFHPKSSDLH LQCGYKVERH LRDDDLVIFN RQPTLHKMSM MGHRVKVLPW STFRMNLSCT SPYNA DFDG DEMNLHVPQS METRAEVENI HITPRQIITP QANKPVMGIV QDTLTAVRKM TKRDVFITRE QVMNLLMFLP TWDAKM PQP CILKPRPLWT GKQIFSLIIP GNVNMIRTHS THPDEEDEGP YKWISPGDTK VMVEHGELIM GILCKKSLGT SAGSLLH IC FLELGHDIAG RFYGNIQTVI NNWLLFEGHS IGIGDTIADP QTYNEIQQAI KKAKDDVINV IQKAHNMELE PTPGNTLR Q TFENKVNRIL NDARDKTGGS AKKSLTEYNN LKAMVVSGSK GSNINISQVI ACVGQQNVEG KRIPYGFRKR TLPHFIKDD YGPESRGFVE NSYLAGLTPS EFYFHAMGGR EGLIDTAVKT AETGYIQRRL IKAMESVMVN YDGTVRNSVG QLIQLRYGED GLCGELVEF QNMPTVKLSN KSFEKRFKFD WSNERLMKKV FTDDVIKEMT DSSEAIQELE AEWDRLVSDR DSLRQIFPNG E SKVVLPCN LQRMIWNVQK IFHINKRLPT DLSPIRVIKG VKTLLERCVI VTGNDRISKQ ANENATLLFQ CLIRSTLCTK YV SEEFRLS TEAFEWLVGE IETRFQQAQA NPGEMVGALA AQSLGEPATQ MTLNTFHFAG VSSKNVTLGV PRLKEIINIS KKP KAPSLT VFLTGGAARD AEKAKNVLCR LEHTTLRKVT ANTAIYYDPD PQRTVISEDQ EFVNVYYEMP DFDPTRISPW LLRI ELDRK RMTDKKLTME QIAEKINVGF GEDLNCIFND DNADKLVLRI RIMNNEENKF QDEDEAVDKM EDDMFLRCIE ANMLS DMTL QGIEAIGKVY MHLPQTDSKK RIVITETGEF KAIGEWLLET DGTSMMKVLS ERDVDPIRTS SNDICEIFQV LGIEAV RKS VEKEMNAVLQ FYGLYVNYRH LALLCDVMTA KGHLMAITRH GINRQDTGAL MRCSFEETVD VLMDAAAHAE TDPMRGV SE NIIMGQLPKM GTGCFDLLLD AEKCRFGI

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #9: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 132.640062 KDa
SequenceString: ENAEEISHEL WQEACWIVIN AYFDEKGLVR QQLDSFDEFI QMSVQRIVED SPAIELQAEA QHTSGEVETP PRFSLKFEQI YLSKPTHWE KDGSPSPMMP NEARLRNLTY SAPLYVDITK TKNVEGLDPV ETQHQKTFIG KIPIMLRSTY CLLSQLTDRD L TELNECPL ...String:
ENAEEISHEL WQEACWIVIN AYFDEKGLVR QQLDSFDEFI QMSVQRIVED SPAIELQAEA QHTSGEVETP PRFSLKFEQI YLSKPTHWE KDGSPSPMMP NEARLRNLTY SAPLYVDITK TKNVEGLDPV ETQHQKTFIG KIPIMLRSTY CLLSQLTDRD L TELNECPL DPGGYFIING SEKVLIAQEK MATNTVYVFS MKDGKYAFKT EIRSCLEHSS RPTSTLWVNM MARGSQNIKK SA IGQRIIA ILPYIKQEIP IMIVFRALGF VADRDILEHI IYDFDDPEMM EMVKPSLDEA FVVQEQNVAL NFIGARGARP GVT KDKRIK YAKEILQKEM LPHVGVSDFC ETKKAYFLGY MVHRLLLASL GRRELDDRDH YGNKRLDLAG PLLAFLFRGL FKNL MKEVR MYTQKFIDRG KDFNLELAIK TNIITDGLRY SLATGNWGDQ KKAHQARAGV SQVLNRLTFA STLSHLRRVN SPIGR DGKL AKPRQLHNTL WGMLCPAETP EGAAVGLVKN LALMAYISVG SQPSPILEFL EEWSMENLEE IAPSAIADAT KIFVNG CWV GIHRDPEQLM ATLRKLRRQM DIIVSEVSMI RDIRDREIRI YTDAGRICRP LLIVENGSLL LKKTHVEMLK ERDYNNY SW QVLVASGVVE YIDTLEEETV MIAMSPYDLK QDKDYAYCTT YTHCEIHPAM ILGVCASIIP FPDHNQSPRN TYQSAMGK Q AMGVYITNFH VRMDTLAHVL YYPMKPLVTT RSMEYLRFRE LPAGINSIVA ILCYTGYNQE DSVILNASAV ERGFFRSVF YRSYKDSENK RVGDQEENFE KPHRGTCQGM RNAHYDKLDD DGIIAPGIRV SGDDVVIGKT ITLPENDDEL DSNTKRFSKR DASTFLRNS ETGIVDQVML TLNSEGYKFC KIRVRSVRIP QIGDKFASRH GQKGTCGIQY RQEDMAFTCE GLAPDIIINP H AIPSRMTI GHLIECLQGK LGSNKGEIGD ATPFNDAVNV QKISTFLQEY GYHLRGNEVM YNGHTGRKIN AQVFLGPTYY QR LKHMVDD KIHSRARGPV QILVRQPMEG RARDGGLRFG EMERDCQISH GAAQFLRERL FEVSDPYRVH ICNFCGLIAI ANL RNNTFE CKGCKNKTQI SQVRLPYAAK LLFQELMSMN IAPRLMVT

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

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Macromolecule #10: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 30.676199 KDa
SequenceString: PYANQPSVQI TELTDDNVKF VLEDTELSVA NSLRRVFIAE TPTLAIDWVQ LEANSTVLSD EFLAHRIGLI PLISDDVVER LQYTRDCIC LDFCPECSVE FTLDVKCSEE QTRHVTTADL KSSNAKVLPV TSRNQGEEDN EYGESNDEIL IIKLRKGQEL K LRAYAKKG ...String:
PYANQPSVQI TELTDDNVKF VLEDTELSVA NSLRRVFIAE TPTLAIDWVQ LEANSTVLSD EFLAHRIGLI PLISDDVVER LQYTRDCIC LDFCPECSVE FTLDVKCSEE QTRHVTTADL KSSNAKVLPV TSRNQGEEDN EYGESNDEIL IIKLRKGQEL K LRAYAKKG FGKEHAKWNP TAGVCFEYDP DNSMRHTLYP KPDEWPKSEH TELEDDQYEA PYNWEAKPNK FFFNVESAGA LK PENIVVM GVQVLKNKLS NLQTQLSHES QN

UniProtKB: GH07456p

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Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 9.73651 KDa
SequenceString:
GGVPKSKRIT TKYMTKYERA RVLGTRALQI AMCAPIMVEL DGETDPLQIA MKELKQKKIP IIIRRYLPDH SYEDWSIDEL IMVD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 16.946137 KDa
SequenceString:
AGVLFEDIFN VKDMDPEGKK FDRVSRLHCE SESFKMDLIL DINSWLYPME LGDKFRLVLA TTLREDGCPD SGEYNPMEHE GTRADSFEY VMYGKIYRIE GDEAHNEASR LSAYVSFGGL LMRLQGDANN LHGFEVDQHM YLLMKRLA

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #13: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.786586 KDa
SequenceString:
GFVGIRFCQE CNNMLYPKED KENKILLYAC RNCDYKQEAD SNCIYVNKIM HEIDELTHIV PDVISDPTLP RTEDHACPKC SHREAVFFQ AQTRRAEEEM RLYYVCTNQN CTHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 7.671124 KDa
SequenceString:
MIIPIRCFTC GKVIGNKWES YLGLLQAEYT EGDALDALGL KRYCCRRMLL GHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #15: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.28824 KDa
SequenceString:
MNAPPTFESF LLYEGEKKII KELDTKVTNA AIFTINKEDH TLGNMIRNQL LKDPNVLFAG YKVPHPLEHK FVIRIQTTAD YSPQEAFMN AITDLLAELS LFEERFKDAI KEKKEGG

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

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Macromolecule #16: DNA-directed RNA polymerase II subunit RPB12

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB12 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 5.647678 KDa
SequenceString:
TAMTYICGEC HHENEMRPRD PIRCRECGYR IMYKKRTKRL VVFDAR

UniProtKB: GEO11084p1

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Macromolecule #17: DNA-directed RNA polymerase II subunit RPB5

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB5 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 24.518332 KDa
SequenceString: MDDEAETYKL WRIRKTIMQL SHDRGYLVTQ DELDQTLEQF KEMFGDKPSE KRPARSDLIV LVAHNDDPTD QMFVFFPEEP KIGIKTIKT YCTRMQEENI HRAIVVVQGG MTPSAKQSLV DMAPKYILEQ FLESELLINI TEHELVPEHV VMTVEEKQEL L SRYKLKEN ...String:
MDDEAETYKL WRIRKTIMQL SHDRGYLVTQ DELDQTLEQF KEMFGDKPSE KRPARSDLIV LVAHNDDPTD QMFVFFPEEP KIGIKTIKT YCTRMQEENI HRAIVVVQGG MTPSAKQSLV DMAPKYILEQ FLESELLINI TEHELVPEHV VMTVEEKQEL L SRYKLKEN MLMRIQAGDP VARYFGLKRG QVVKIIRSSE TAGRYISYRL VC

UniProtKB: RPB5 homolog

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 8 / 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

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
10.0 mMHEPES-HClHEPES
5.0 percentGlycerolGlycerol
1.0 mMEDTAEDTA
350.0 ug/mLFLAGFLAG peptide

Details: 10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV
Detailsdouble FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 4 / Number real images: 31103 / Average electron dose: 50.65 e/Å2
Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was ...Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 4197404
Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D ...Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D classification of the data representing Pol II and nucleosome subsets, respectively.
Startup modelType of model: INSILICO MODEL / In silico model: 'Ab initio' function in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1)
Details: The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite ...Details: The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite map of the two locally refined entities.
Number images used: 36552
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: 'Non-Uniform Refinement' in cryoSPARC

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Atomic model buiding 1

DetailsThe model was based on individual models from this study: octameric nucleosome and Pol II. The models were rigid-body fit into the composite structure, connected and fixed in Coot and Phenix.
RefinementProtocol: AB INITIO MODEL / Overall B value: 50
Output model

PDB-9mu9:
Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

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