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- PDB-8iuh: RNA polymerase III pre-initiation complex open complex 1 -

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Basic information

Entry
Database: PDB / ID: 8iuh
TitleRNA polymerase III pre-initiation complex open complex 1
Components
  • (DNA (81-MER)) x 2
  • (DNA-directed RNA polymerase III subunit ...) x 10
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Transcription factor ...) x 2
  • (snRNA-activating protein complex subunit ...) x 3
  • TATA-box-binding protein
KeywordsTRANSCRIPTION / RNA polymerase III / SNAPc complex
Function / homology
Function and homology information


transcription preinitiation complex assembly / snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly ...transcription preinitiation complex assembly / snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / DNA/RNA hybrid binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase I / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / regulation of transcription by RNA polymerase III / RPAP3/R2TP/prefoldin-like complex / RNA polymerase III general transcription initiation factor activity / DNA polymerase III complex / RNA polymerase I core promoter sequence-specific DNA binding / Cytosolic sensors of pathogen-associated DNA / 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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / positive regulation of innate immune response / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / nucleobase-containing compound metabolic process / RNA Polymerase I Transcription Termination / transcription preinitiation complex / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / aryl hydrocarbon receptor binding / transcription by RNA polymerase I / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / positive regulation of transcription initiation by RNA polymerase II / transcription elongation by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase II core promoter sequence-specific DNA binding / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / core promoter sequence-specific DNA binding / Formation of RNA Pol II elongation complex / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / TBP-class protein binding / positive regulation of interferon-beta production / mRNA Splicing - Major Pathway / acrosomal vesicle / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / DNA-templated transcription initiation / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs
Similarity search - Function
: / BRF2-like, C-terminal cyclin repeat / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / : / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / DNA-directed RNA polymerase III subunit RPC5, C-terminal ...: / BRF2-like, C-terminal cyclin repeat / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / : / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / DNA-directed RNA polymerase III subunit RPC5, C-terminal / DNA-directed RNA polymerase III subunit RPC5 C-terminal / DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RPC5 protein / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / POLR3C, C-terminal winged-helix domain / Myb-like domain profile. / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / DNA-directed RNA polymerase, subunit E/RPC8 / Myb-like DNA-binding domain / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / Myb-type HTH DNA-binding domain profile. / SANT domain / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Myb domain / TBP domain superfamily / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / SANT/Myb domain / Cyclin-like superfamily / Zinc finger TFIIS-type signature. / HRDC-like superfamily / 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 / 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 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, subunit RPB6 / 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.
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / : / DNA / DNA (> 10) / DNA (> 100) / Transcription factor TFIIIB component B'' homolog / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerase III subunit RPC9 ...IRON/SULFUR CLUSTER / : / DNA / DNA (> 10) / DNA (> 100) / Transcription factor TFIIIB component B'' homolog / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / TATA-box-binding protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex subunit 4 / snRNA-activating protein complex subunit 3 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / Transcription factor IIIB 50 kDa subunit / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC10 / DNA-directed RNA polymerase III subunit RPC8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHou, H. / Jin, Q. / Ren, Y. / Wang, Q. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Cell Res / Year: 2023
Title: Structure of the SNAPc-bound RNA polymerase III preinitiation complex.
Authors: Haifeng Hou / Qianwei Jin / Yulei Ren / Zhenguo Chen / Qianmin Wang / Yanhui Xu /
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: snRNA-activating protein complex subunit 1
3: snRNA-activating protein complex subunit 3
4: snRNA-activating protein complex subunit 4
A: DNA-directed RNA polymerase III subunit RPC1
B: DNA-directed RNA polymerase III subunit RPC2
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase III subunit RPC9
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase III subunit RPC8
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase III subunit RPC10
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase III subunit RPC5
N: DNA-directed RNA polymerase III subunit RPC4
O: DNA-directed RNA polymerase III subunit RPC3
P: DNA-directed RNA polymerase III subunit RPC6
Q: DNA-directed RNA polymerase III subunit RPC7
U: TATA-box-binding protein
V: Transcription factor IIIB 50 kDa subunit
W: Transcription factor TFIIIB component B'' homolog
X: DNA (81-MER)
Y: DNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,614,63135
Polymers1,613,73225
Non-polymers89910
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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SnRNA-activating protein complex subunit ... , 3 types, 3 molecules 134

#1: Protein snRNA-activating protein complex subunit 1 / SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE- ...SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE-binding factor subunit gamma / PTF subunit gamma / Small nuclear RNA-activating complex polypeptide 1 / snRNA-activating protein complex 43 kDa subunit / SNAPc 43 kDa subunit


Mass: 43074.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC1, SNAP43 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q16533
#2: Protein snRNA-activating protein complex subunit 3 / SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding ...SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding factor subunit beta / PTF subunit beta / Small nuclear RNA-activating complex polypeptide 3 / snRNA-activating protein complex 50 kDa subunit / SNAPc 50 kDa subunit


Mass: 46812.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC3, SNAP50 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q92966
#3: Protein snRNA-activating protein complex subunit 4 / SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE- ...SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE-binding factor subunit alpha / PTF subunit alpha / snRNA-activating protein complex 190 kDa subunit / SNAPc 190 kDa subunit


Mass: 159645.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC4, SNAP190 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5SXM2

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DNA-directed RNA polymerase III subunit ... , 10 types, 10 molecules ABDGIMNOPQ

#4: Protein DNA-directed RNA polymerase III subunit RPC1 / RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / DNA-directed RNA ...RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / DNA-directed RNA polymerase III subunit A / RNA polymerase III 155 kDa subunit / RPC155 / RNA polymerase III subunit C160


Mass: 155860.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3A / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O14802, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase III subunit RPC2 / RNA polymerase III subunit C2 / C128 / DNA-directed RNA polymerase III 127.6 kDa polypeptide / DNA- ...RNA polymerase III subunit C2 / C128 / DNA-directed RNA polymerase III 127.6 kDa polypeptide / DNA-directed RNA polymerase III subunit B


Mass: 127953.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3B / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NW08, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit C9 / Calcitonin gene-related peptide-receptor component protein / HsC17


Mass: 16893.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRCP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O75575
#10: Protein DNA-directed RNA polymerase III subunit RPC8 / RNA polymerase III subunit C8 / DNA-directed RNA polymerase III subunit H / RNA polymerase III ...RNA polymerase III subunit C8 / DNA-directed RNA polymerase III subunit H / RNA polymerase III subunit 22.9 kDa subunit / RPC22.9


Mass: 22938.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3H, KIAA1665, RPC8 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y535
#12: Protein DNA-directed RNA polymerase III subunit RPC10 / RNA polymerase III subunit C10 / DNA-directed RNA polymerase III subunit K / RNA polymerase III 12. ...RNA polymerase III subunit C10 / DNA-directed RNA polymerase III subunit K / RNA polymerase III 12.5 kDa subunit / RPC12.5 / RNA polymerase III subunit C11 / HsC11p / RPC11 / hRPC11


Mass: 12338.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3K, RPC11, My010 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y2Y1
#16: Protein DNA-directed RNA polymerase III subunit RPC5 / RNA polymerase III subunit C5 / DNA-directed RNA polymerase III 80 kDa polypeptide


Mass: 80004.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3E, KIAA1452 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NVU0
#17: Protein DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III subunit C4 / DNA-directed RNA polymerase III subunit D / Protein BN51 / RNA ...RNA polymerase III subunit C4 / DNA-directed RNA polymerase III subunit D / Protein BN51 / RNA polymerase III 47 kDa subunit / RPC53 homolog


Mass: 35195.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3D, BN51, BN51T / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P05423
#18: Protein DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit C3 / DNA-directed RNA polymerase III subunit C / RNA polymerase III 62 ...RNA polymerase III subunit C3 / DNA-directed RNA polymerase III subunit C / RNA polymerase III 62 kDa subunit / RPC62


Mass: 60692.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BUI4
#19: Protein DNA-directed RNA polymerase III subunit RPC6 / RNA polymerase III subunit C6 / DNA-directed RNA polymerase III subunit F / RNA polymerase III 39 ...RNA polymerase III subunit C6 / DNA-directed RNA polymerase III subunit F / RNA polymerase III 39 kDa subunit / RPC39


Mass: 35726.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3F / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9H1D9
#20: Protein DNA-directed RNA polymerase III subunit RPC7 / RNA polymerase III subunit C7 / DNA-directed RNA polymerase III subunit G / RNA polymerase III 32 ...RNA polymerase III subunit C7 / DNA-directed RNA polymerase III subunit G / RNA polymerase III 32 kDa apha subunit / RPC32-alpha / RNA polymerase III 32 kDa subunit / RPC32


Mass: 25953.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR3G / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15318

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#6: Protein DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa ...RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / RPA40 / RPA39 / RPC40


Mass: 39301.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR1C, POLR1E / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15160
#14: Protein DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA ...RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA polymerase I 16 kDa subunit / RPA16 / RPC16 / hRPA19


Mass: 15259.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR1D / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DPB6

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

#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


Mass: 24584.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2E / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P19388
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14491.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2F, POLRF / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61218
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2H / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P52434
#13: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


Mass: 7655.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2L / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P62875
#15: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2K / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P53803

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Protein , 1 types, 1 molecules U

#21: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226

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Transcription factor ... , 2 types, 2 molecules VW

#22: Protein Transcription factor IIIB 50 kDa subunit / TFIIIB50 / hTFIIIB50 / B-related factor 2 / BRF-2 / hBRFU


Mass: 46587.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRF2, BRFU, PRO1470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAW0
#23: Protein Transcription factor TFIIIB component B'' homolog / Transcription factor IIIB 150 / TFIIIB150 / Transcription factor-like nuclear regulator


Mass: 294301.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDP1, KIAA1241, KIAA1689, TFNR / Production host: Escherichia coli (E. coli) / References: UniProt: A6H8Y1

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DNA chain , 2 types, 2 molecules XY

#24: DNA chain DNA (81-MER)


Mass: 143512.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 37562
#25: DNA chain DNA (81-MER)


Mass: 143039.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 37562

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Non-polymers , 3 types, 10 molecules

#26: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#27: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN

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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
1RNA polymerase III pre-initiation complex closed complex 1COMPLEX#1-#250MULTIPLE SOURCES
2DNA-directed RNA polymerase III, SNAPCCOMPLEX#1-#201RECOMBINANT
3TFIIIBCOMPLEX#21-#231RECOMBINANT
4DNACOMPLEX#24-#251SYNTHETIC
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Escherichia coli (E. coli)562
12Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107630 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00259698
ELECTRON MICROSCOPYf_angle_d0.39981288
ELECTRON MICROSCOPYf_dihedral_angle_d13.11723037
ELECTRON MICROSCOPYf_chiral_restr0.0379051
ELECTRON MICROSCOPYf_plane_restr0.0039902

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