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- PDB-7nky: RNA Polymerase II-Spt4/5-nucleosome-FACT structure -

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Basic information

Entry
Database: PDB / ID: 7nky
TitleRNA Polymerase II-Spt4/5-nucleosome-FACT structure
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (FACT complex subunit ...FACT (biology)) x 2
  • Chromatin elongation factor SPT4
  • DNA (138-MER)
  • DNA (148-MER)
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')
  • Transcription elongation factor SPT5
KeywordsTRANSCRIPTION / Chromatin / nucleosome / elongation / histone chaperone
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / nucleosome organization / RPB4-RPB7 complex / replication fork protection complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of DNA-templated transcription, elongation ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / nucleosome organization / RPB4-RPB7 complex / replication fork protection complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of DNA-templated transcription, elongation / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase II transcription / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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-templated transcription / termination of RNA polymerase III transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase III activity / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / tRNA transcription by RNA polymerase III / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / chromosome, centromeric region / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / RNA polymerase II activity / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / P-body / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / ribonucleoside binding / DNA-templated DNA replication / mRNA processing / DNA-directed 5'-3' RNA polymerase activity / peroxisome / DNA-directed RNA polymerase / cytoplasmic stress granule / structural constituent of chromatin / nucleosome / nucleosome assembly / ribosome biogenesis / single-stranded DNA binding / chromosome / chromatin organization / transcription by RNA polymerase II / DNA replication / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / protein heterodimerization activity / nucleotide binding / mRNA binding / DNA repair / chromatin / nucleolus / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / FACT complex subunit Spt16 domain ...: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH 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 chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Creatinase/Aminopeptidase P/Spt16, N-terminal / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / 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 subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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, 7 kDa subunit / DNA-directed RNA polymerase subunit Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / FACT complex subunit POB3 / Transcription elongation factor SPT4 / Transcription elongation factor SPT5 / Histone H2B 1.1 / DNA-directed RNA polymerase II subunit RPB1 ...DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / FACT complex subunit POB3 / Transcription elongation factor SPT4 / Transcription elongation factor SPT5 / Histone H2B 1.1 / DNA-directed RNA polymerase II subunit RPB1 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / FACT complex subunit SPT16 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
synthetic RNA (others)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFarnung, L. / Ochmann, M. / Engeholm, M. / Cramer, P.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)693023European Union
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis of nucleosome transcription mediated by Chd1 and FACT.
Authors: Lucas Farnung / Moritz Ochmann / Maik Engeholm / Patrick Cramer /
Abstract: Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is ...Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA.
History
DepositionFeb 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
P: RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')
N: DNA (138-MER)
T: DNA (148-MER)
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Y: Chromatin elongation factor SPT4
Z: Transcription elongation factor SPT5
D: DNA-directed RNA polymerase II subunit RPB4
G: DNA-directed RNA polymerase II subunit RPB7
O: FACT complex subunit POB3
Q: FACT complex subunit SPT16
a: Histone H3.2
b: Histone H4
c: Histone H2A type 1
d: Histone H2B 1.1
e: Histone H3.2
f: Histone H4
g: Histone H2A type 1
h: Histone H2B 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,026,14837
Polymers1,025,53527
Non-polymers61310
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules P

#1: RNA chain RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')


Mass: 4913.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic RNA (others)

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DNA chain , 2 types, 2 molecules NT

#2: DNA chain DNA (138-MER)


Mass: 42792.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (148-MER)


Mass: 45537.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCIKDG

#4: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P04050, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P08518, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P16370
#10: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P27999
#12: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P38902
#16: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P20433
#17: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P34087

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P20434
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P20435
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P20436
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P22139
#13: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 / References: UniProt: P40422

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Protein , 6 types, 10 molecules YZaebfcgdh

#14: Protein Chromatin elongation factor SPT4 / Transcription elongation factor SPT4


Mass: 11168.772 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ5464
Gene: PACBIOSEQ_LOCUS2707, PACBIOSEQ_LOCUS2757, SCNYR20_0003027800, SCP684_0002027900
Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5PX04
#15: Protein Transcription elongation factor SPT5


Mass: 115929.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS4816 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6L0ZFJ2
#20: Protein Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#21: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#22: Protein Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#23: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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FACT complex subunit ... , 2 types, 2 molecules OQ

#18: Protein FACT complex subunit POB3 / FACT (biology)


Mass: 63068.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BJ5464
Gene: PACBIOSEQ_LOCUS4754, SCNYR20_0006005900, SCP684_0006005800
Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5PUM6
#19: Protein FACT complex subunit SPT16 / FACT (biology) / Cell division control protein 68 / Facilitates chromatin transcription complex subunit SPT16 / ...Cell division control protein 68 / Facilitates chromatin transcription complex subunit SPT16 / Suppressor of Ty protein 16


Mass: 118776.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: BJ5464 / Gene: SPT16, CDC68, SSF1, YGL207W / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32558

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Non-polymers , 2 types, 10 molecules

#24: Chemical
ChemComp-ZN / ZINC ION


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


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

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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
1Complex of RNA polymerase II-Spt4/5-FACT-nucleosomeCOMPLEX#1-#230MULTIPLE SOURCES
2RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3')COMPLEX#11SYNTHETIC
3DNA (138-MER)COMPLEX#21SYNTHETIC
4DNA (148-MER)COMPLEX#31SYNTHETIC
5DNA-directed RNA polymerase II subunit RPB1PolymeraseCOMPLEX#41NATURAL
6DNA-directed RNA polymerase II subunit RPB2PolymeraseCOMPLEX#51NATURAL
7DNA-directed RNA polymerase II subunit RPB3PolymeraseCOMPLEX#61NATURAL
8DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymeraseCOMPLEX#71NATURAL
9DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymeraseCOMPLEX#81NATURAL
10DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymeraseCOMPLEX#91NATURAL
11DNA-directed RNA polymerase II subunit RPB9PolymeraseCOMPLEX#101NATURAL
12DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymeraseCOMPLEX#111NATURAL
13DNA-directed RNA polymerase II subunit RPB11PolymeraseCOMPLEX#121NATURAL
14DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymeraseCOMPLEX#131NATURAL
15Chromatin elongation factor SPT4COMPLEX#141RECOMBINANT
16Transcription elongation factor SPT5COMPLEX#151RECOMBINANT
17DNA-directed RNA polymerase II subunit RPB4PolymeraseCOMPLEX#161NATURAL
18DNA-directed RNA polymerase II subunit RPB7PolymeraseCOMPLEX#171RECOMBINANT
19FACT complex subunit POB3FACT (biology)COMPLEX#181RECOMBINANT
20FACT complex subunit SPT16FACT (biology)COMPLEX#191RECOMBINANT
21Histone H3.2COMPLEX#201RECOMBINANT
22Histone H4COMPLEX#211RECOMBINANT
23Histone H2A type 1COMPLEX#221RECOMBINANT
24Histone H2B 1.1COMPLEX#231RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
15Saccharomyces cerevisiae (brewer's yeast)4932
26Saccharomyces cerevisiae (brewer's yeast)4932
37Saccharomyces cerevisiae (brewer's yeast)4932
48Saccharomyces cerevisiae (brewer's yeast)4932
59Saccharomyces cerevisiae (brewer's yeast)4932
610Saccharomyces cerevisiae (brewer's yeast)4932
711Saccharomyces cerevisiae (brewer's yeast)4932
811Saccharomyces cerevisiae (brewer's yeast)4932
913Saccharomyces cerevisiae (brewer's yeast)4932
1014Saccharomyces cerevisiae (brewer's yeast)4932
1115Saccharomyces cerevisiae (brewer's yeast)4932
1216Saccharomyces cerevisiae (brewer's yeast)4932
1317Saccharomyces cerevisiae (brewer's yeast)4932
1418Saccharomyces cerevisiae (brewer's yeast)4932
1519Saccharomyces cerevisiae (brewer's yeast)4932
1620Saccharomyces cerevisiae (brewer's yeast)4932
1721Xenopus laevis (African clawed frog)8355
1822Xenopus laevis (African clawed frog)8355
1923Xenopus laevis (African clawed frog)8355
2024Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
115Trichoplusia ni (cabbage looper)7111
216Trichoplusia ni (cabbage looper)7111
319Trichoplusia ni (cabbage looper)7111
420Trichoplusia ni (cabbage looper)7111
521Escherichia coli (E. coli)562
622Escherichia coli (E. coli)562
723Escherichia coli (E. coli)562
824Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy
Image recordingElectron dose: 40.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47138 / Symmetry type: POINT

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