8ITY | pdb_00008ity

human RNA polymerase III pre-initiation complex closed DNA 1

PDB DOI: https://doi.org/10.2210/pdb8ITY/pdb
EM Map EMD-35712: EMDB EMDataResource
NAKB: 8ITY

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes

Deposited: 2023-03-23 Released: 2023-06-07
Deposition Author(s): Hou, H., Jin, Q., Ren, Y., Wang, Q., Xu, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the SNAPc-bound RNA polymerase III preinitiation complex.

Hou, H., Jin, Q., Ren, Y., Chen, Z., Wang, Q., Xu, Y.

(2023) Cell Res 33: 565-568

PubMed: 37165065 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00819-x
Primary Citation Related Structures:
8ITY, 8IUE, 8IUH

Organizational Affiliation

Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 1,614.57 kDa
Atom Count: 57,140
Modeled Residue Count: 6,885
Deposited Residue Count: 12,730
Unique protein chains: 23
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
snRNA-activating protein complex subunit 1	A [auth 1]	368	Homo sapiens	Mutation(s): 0 Gene Names: SNAPC1, SNAP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q16533 (Homo sapiens) Explore Q16533 Go to UniProtKB: Q16533
PHAROS: Q16533 GTEx: ENSG00000023608
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16533
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
snRNA-activating protein complex subunit 3	B [auth 3]	411	Homo sapiens	Mutation(s): 0 Gene Names: SNAPC3, SNAP50
UniProt & NIH Common Fund Data Resources
Find proteins for Q92966 (Homo sapiens) Explore Q92966 Go to UniProtKB: Q92966
PHAROS: Q92966 GTEx: ENSG00000164975
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92966
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
snRNA-activating protein complex subunit 4	C [auth 4]	1,469	Homo sapiens	Mutation(s): 0 Gene Names: SNAPC4, SNAP190
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SXM2 (Homo sapiens) Explore Q5SXM2 Go to UniProtKB: Q5SXM2
PHAROS: Q5SXM2 GTEx: ENSG00000165684
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SXM2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC1	D [auth A]	1,390	Homo sapiens	Mutation(s): 0 Gene Names: POLR3A EC: 2.7.7.6
UniProt & NIH Common Fund Data Resources
Find proteins for O14802 (Homo sapiens) Explore O14802 Go to UniProtKB: O14802
PHAROS: O14802 GTEx: ENSG00000148606
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14802
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC2	E [auth B]	1,133	Homo sapiens	Mutation(s): 0 Gene Names: POLR3B EC: 2.7.7.6
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Find proteins for Q9NW08 (Homo sapiens) Explore Q9NW08 Go to UniProtKB: Q9NW08
PHAROS: Q9NW08 GTEx: ENSG00000013503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NW08
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I and III subunit RPAC1	F [auth C]	346	Homo sapiens	Mutation(s): 0 Gene Names: POLR1C, POLR1E
UniProt & NIH Common Fund Data Resources
Find proteins for O15160 (Homo sapiens) Explore O15160 Go to UniProtKB: O15160
PHAROS: O15160 GTEx: ENSG00000171453
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15160
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC9	G [auth D]	148	Homo sapiens	Mutation(s): 0 Gene Names: CRCP
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Find proteins for O75575 (Homo sapiens) Explore O75575 Go to UniProtKB: O75575
PHAROS: O75575 GTEx: ENSG00000241258
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75575
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	H [auth E]	210	Homo sapiens	Mutation(s): 0 Gene Names: POLR2E
UniProt & NIH Common Fund Data Resources
Find proteins for P19388 (Homo sapiens) Explore P19388 Go to UniProtKB: P19388
PHAROS: P19388 GTEx: ENSG00000099817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19388
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	I [auth F]	127	Homo sapiens	Mutation(s): 0 Gene Names: POLR2F, POLRF
UniProt & NIH Common Fund Data Resources
Find proteins for P61218 (Homo sapiens) Explore P61218 Go to UniProtKB: P61218
PHAROS: P61218 GTEx: ENSG00000100142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61218
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC8	J [auth G]	204	Homo sapiens	Mutation(s): 0 Gene Names: POLR3H, KIAA1665, RPC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y535 (Homo sapiens) Explore Q9Y535 Go to UniProtKB: Q9Y535
PHAROS: Q9Y535 GTEx: ENSG00000100413
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y535
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	K [auth H]	150	Homo sapiens	Mutation(s): 0 Gene Names: POLR2H
UniProt & NIH Common Fund Data Resources
Find proteins for P52434 (Homo sapiens) Explore P52434 Go to UniProtKB: P52434
PHAROS: P52434 GTEx: ENSG00000163882
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52434
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC10	L [auth I]	108	Homo sapiens	Mutation(s): 1 Gene Names: POLR3K, RPC11, My010
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Y1 (Homo sapiens) Explore Q9Y2Y1 Go to UniProtKB: Q9Y2Y1
PHAROS: Q9Y2Y1 GTEx: ENSG00000161980
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2Y1
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	M [auth J]	67	Homo sapiens	Mutation(s): 0 Gene Names: POLR2L
UniProt & NIH Common Fund Data Resources
Find proteins for P62875 (Homo sapiens) Explore P62875 Go to UniProtKB: P62875
PHAROS: P62875 GTEx: ENSG00000177700
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62875
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I and III subunit RPAC2	N [auth K]	133	Homo sapiens	Mutation(s): 0 Gene Names: POLR1D
UniProt & NIH Common Fund Data Resources
Find proteins for P0DPB6 (Homo sapiens) Explore P0DPB6 Go to UniProtKB: P0DPB6
PHAROS: P0DPB6 GTEx: ENSG00000186184
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DPB6
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	O [auth L]	58	Homo sapiens	Mutation(s): 0 Gene Names: POLR2K
UniProt & NIH Common Fund Data Resources
Find proteins for P53803 (Homo sapiens) Explore P53803 Go to UniProtKB: P53803
PHAROS: P53803 GTEx: ENSG00000147669
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53803
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC5	P [auth M]	708	Homo sapiens	Mutation(s): 0 Gene Names: POLR3E, KIAA1452
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVU0 (Homo sapiens) Explore Q9NVU0 Go to UniProtKB: Q9NVU0
PHAROS: Q9NVU0 GTEx: ENSG00000058600
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NVU0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC4	Q [auth N]	317	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05423 (Homo sapiens) Explore P05423 Go to UniProtKB: P05423
PHAROS: P05423 GTEx: ENSG00000168495
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05423
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC3	R [auth O]	534	Homo sapiens	Mutation(s): 0 Gene Names: POLR3C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUI4 (Homo sapiens) Explore Q9BUI4 Go to UniProtKB: Q9BUI4
PHAROS: Q9BUI4 GTEx: ENSG00000186141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BUI4
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC6	S [auth P]	316	Homo sapiens	Mutation(s): 0 Gene Names: POLR3F
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1D9 (Homo sapiens) Explore Q9H1D9 Go to UniProtKB: Q9H1D9
PHAROS: Q9H1D9 GTEx: ENSG00000132664
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H1D9
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase III subunit RPC7	T [auth Q]	223	Homo sapiens	Mutation(s): 0 Gene Names: POLR3G
UniProt & NIH Common Fund Data Resources
Find proteins for O15318 (Homo sapiens) Explore O15318 Go to UniProtKB: O15318
PHAROS: O15318 GTEx: ENSG00000113356
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15318
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box-binding protein	U	339	Homo sapiens	Mutation(s): 0 Gene Names: TBP, GTF2D1, TF2D, TFIID
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens) Explore P20226 Go to UniProtKB: P20226
PHAROS: P20226 GTEx: ENSG00000112592
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20226
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor IIIB 50 kDa subunit	V	419	Homo sapiens	Mutation(s): 0 Gene Names: BRF2, BRFU, PRO1470
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAW0 (Homo sapiens) Explore Q9HAW0 Go to UniProtKB: Q9HAW0
GTEx: ENSG00000104221
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HAW0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor TFIIIB component B'' homolog	W	2,624	Homo sapiens	Mutation(s): 0 Gene Names: BDP1, KIAA1241, KIAA1689, TFNR
UniProt & NIH Common Fund Data Resources
Find proteins for A6H8Y1 (Homo sapiens) Explore A6H8Y1 Go to UniProtKB: A6H8Y1
PHAROS: A6H8Y1 GTEx: ENSG00000145734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6H8Y1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 24
DNA (82-MER)	X	464	Homo sapiens
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Molecule	Chains	Length	Organism
Entity ID: 25
DNA (82-MER)	Y	464	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain GA [auth P] MOL2 format, chain GA [auth P] mmCIF format, chain GA [auth P]	GA [auth P]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain GA [auth P] Interactions & Density Focus chain GA [auth P]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain HA [auth V] SDF format, chain FA [auth L] SDF format, chain EA [auth J] SDF format, chain DA [auth I] SDF format, chain CA [auth B] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain HA [auth V] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain HA [auth V] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth A]	AA [auth A] CA [auth B] DA [auth I] EA [auth J] FA [auth L] AA [auth A], CA [auth B], DA [auth I], EA [auth J], FA [auth L], HA [auth V], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain CA [auth B] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth L] Focus chain HA [auth V] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth B] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth L] Focus chain HA [auth V] Focus chain Z [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain BA [auth A]	BA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]