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- PDB-6ted: Structure of complete, activated transcription complex Pol II-DSI... -

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Entry
Database: PDB / ID: 6ted
TitleStructure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
Components
  • (DNA-directed RNA polymerase ...) x 3
  • (RNA polymerase II subunit ...) x 5
  • (RNA polymerase-associated protein ...) x 3
  • (Transcription elongation factor ...) x 3
  • (Uncharacterized ...) x 3
  • DNA (37-MER)
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3
  • Parafibromin
  • RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
  • RNA polymerase II-associated factor 1 homolog
  • Template DNA
  • WD repeat-containing protein 61
KeywordsTRANSCRIPTION / Polymerase / elongation complex / RNA / DNA
Function / homology
Function and homology information


endodermal cell fate commitment / Ski complex / regulation of isotype switching / RNA polymerase II C-terminal domain phosphoserine binding / mRNA decay by 3' to 5' exoribonuclease / positive regulation of mRNA 3'-end processing / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of DNA-templated transcription, elongation / : ...endodermal cell fate commitment / Ski complex / regulation of isotype switching / RNA polymerase II C-terminal domain phosphoserine binding / mRNA decay by 3' to 5' exoribonuclease / positive regulation of mRNA 3'-end processing / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of DNA-templated transcription, elongation / : / transcription pausing by RNA polymerase II / negative regulation of myeloid cell differentiation / regulation of muscle cell differentiation / positive regulation of cell cycle G1/S phase transition / DSIF complex / transcription elongation factor complex / nucleosome organization / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / mRNA Splicing - Major Pathway / mRNA Polyadenylation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription elongation-coupled chromatin remodeling / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / interleukin-6-mediated signaling pathway / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / organelle membrane / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / 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 / protein localization to nucleus / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / negative regulation of fibroblast proliferation / positive regulation of translational initiation / mRNA transport / nuclear-transcribed mRNA catabolic process / Tat-mediated elongation of the HIV-1 transcript / positive regulation of Wnt signaling pathway / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / cell surface receptor signaling pathway via JAK-STAT / Dengue virus activates/modulates innate and adaptive immune responses / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase II Transcription Elongation / RNA polymerase I complex / nucleosome binding / RNA polymerase III complex / Formation of RNA Pol II elongation complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / transcription-coupled nucleotide-excision repair / translation initiation factor binding / RNA splicing / SH2 domain binding / DNA-templated transcription elongation / rescue of stalled cytosolic ribosome / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II
Similarity search - Function
Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Leo1-like protein ...Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / HHH domain 9 / HHH domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Leo1-like protein / Leo1-like protein / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / : / RNA pol II accessory factor, Cdc73 family, C-terminal / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Spt5, KOW domain repeat 6 / : / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Tetratricopeptide repeat / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Gyrase A; domain 2 - #140 / RNA-binding domain, S1 / : / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Tetratricopeptide repeat / RuvA domain 2-like / RNA polymerase Rpb1, domain 3 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / Enzyme I; Chain A, domain 2 / NusG, N-terminal domain superfamily / Tetratricopeptide repeat / Gyrase A; domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / S1 domain profile. / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / Uncharacterized protein / : / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC2 ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / Uncharacterized protein / : / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / Parafibromin / RNA polymerase-associated protein CTR9 homolog / Transcription elongation factor SPT6 / RNA polymerase II-associated factor 1 homolog / RNA polymerase-associated protein LEO1 / RNA polymerase-associated protein RTF1 homolog / Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVos, S.M. / Farnung, L. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
European Research Council693023 Germany
German Research FoundationSFB860 Germany
German Research FoundationSFB860 Germany
Volkswagen Foundation Germany
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
Authors: Seychelle M Vos / Lucas Farnung / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation ...Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II subunit C
D: RNA polymerase II subunit D
E: RNA polymerase II subunit E
F: RNA polymerase II subunit F
G: RNA polymerase II subunit G
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
M: Transcription elongation factor SPT6
N: DNA (37-MER)
P: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')
Q: RNA polymerase-associated protein CTR9 homolog
R: RNA polymerase-associated protein RTF1 homolog
T: Template DNA
U: RNA polymerase-associated protein LEO1
V: RNA polymerase II-associated factor 1 homolog
W: WD repeat-containing protein 61
X: Parafibromin
Y: Transcription elongation factor SPT4
Z: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,351,86834
Polymers1,351,25524
Non-polymers61310
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area115260 Å2
ΔGint-689 kcal/mol
Surface area283750 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Protein DNA-directed RNA polymerase subunit


Mass: 219049.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A480RVL6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 142426.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899

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RNA polymerase II subunit ... , 5 types, 5 molecules CDEFG

#3: Protein RNA polymerase II subunit C


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#4: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4
#5: Protein RNA polymerase II subunit E


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7
#6: Protein RNA polymerase II subunit F


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8
#7: Protein RNA polymerase II subunit G


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJZ9

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Protein , 4 types, 4 molecules HVWX

#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2
#20: Protein RNA polymerase II-associated factor 1 homolog / hPAF1 / Pancreatic differentiation protein 2


Mass: 60052.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAF1, PD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N7H5
#21: Protein WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog / SKI8 homolog / Ski8


Mass: 33617.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9GZS3
#22: Protein Parafibromin / Cell division cycle protein 73 homolog / Hyperparathyroidism 2 protein


Mass: 60673.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC73, C1orf28, HRPT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1J9

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Uncharacterized ... , 3 types, 3 molecules JKL

#10: Protein Uncharacterized protein


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B432, UniProt: A0A4X1VYD0*PLUS
#11: Protein Uncharacterized protein


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4
#12: Protein Uncharacterized protein


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51

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Transcription elongation factor ... , 3 types, 3 molecules MYZ

#13: Protein Transcription elongation factor SPT6 / hSPT6 / Histone chaperone suppressor of Ty6 / Tat-cotransactivator 2 protein / Tat-CT2 protein


Mass: 199602.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, KIAA0162, SPT6H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85
#23: Protein Transcription elongation factor SPT4 / hSPT4 / DRB sensitivity-inducing factor 14 kDa subunit / DSIF p14 / DRB sensitivity-inducing factor ...hSPT4 / DRB sensitivity-inducing factor 14 kDa subunit / DSIF p14 / DRB sensitivity-inducing factor small subunit / DSIF small subunit


Mass: 13508.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, SPT4H, SUPT4H / Production host: Escherichia coli (E. coli) / References: UniProt: P63272
#24: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121225.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / References: UniProt: O00267

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain DNA (37-MER)


Mass: 14932.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain Template DNA


Mass: 14672.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules P

#15: RNA chain RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')


Mass: 14843.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA polymerase-associated protein ... , 3 types, 3 molecules QRU

#16: Protein RNA polymerase-associated protein CTR9 homolog / SH2 domain-binding protein 1


Mass: 134510.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PD62
#17: Protein RNA polymerase-associated protein RTF1 homolog


Mass: 80733.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92541
#19: Protein RNA polymerase-associated protein LEO1 / Replicative senescence down-regulated leo1-like protein


Mass: 75514.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LEO1, RDL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVC0

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Non-polymers , 2 types, 10 molecules

#25: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#26: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complete EC*COMPLEX#1-#240MULTIPLE SOURCES
2Pig DNA/RNA polymerase subunitsCOMPLEX#1-#121NATURAL
3Human transcription factors and associated proteinsCOMPLEX#13, #16-#17, #19-#221RECOMBINANT
4DNA/RNACOMPLEX#14-#15, #181RECOMBINANT
5Transcription elongation factor SPT4 and SPT5COMPLEX#23-#241RECOMBINANT
Molecular weightValue: 1.34 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34synthetic construct (others)32630
45Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Trichoplusia ni (cabbage looper)7111
24synthetic construct (others)32630
35Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMNaCl1
220 mMNa-HEPES1
31 mMDTT1
420 mMTRIS-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 13679
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
1Warpparticle selection
2EPUimage acquisition
4WarpCTF correction
7UCSF Chimeramodel fitting
8NAMDmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 611983
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 446195 / Symmetry type: POINT
Atomic model buildingB value: 115 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16GMH

6gmh

16GMH1PDBexperimental model
24L1U

4l1u

14L1U2PDBexperimental model
36AFO

6afo

16AFO3PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02558407
ELECTRON MICROSCOPYf_angle_d1.34279040
ELECTRON MICROSCOPYf_dihedral_angle_d8.94834045
ELECTRON MICROSCOPYf_chiral_restr0.0838370
ELECTRON MICROSCOPYf_plane_restr0.00810156

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Jul 12, 2017. Major update of PDB

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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