8UMI | pdb_00008umi

consensus map of PICdeltaTFIIK form1

PDB DOI: https://doi.org/10.2210/pdb8UMI/pdb
EM Map EMD-42380: EMDB EMDataResource
NAKB: 8UMI

Classification: TRANSCRIPTION
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-10-17 Released: 2024-10-30
Deposition Author(s): Yang, C., Murakami, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

consensus map of PICdeltaTFIIK form1

Yang, C., Murakami, K.

To be published.

Macromolecule Content

Total Structure Weight: 1,336.83 kDa
Atom Count: 70,523
Modeled Residue Count: 8,668
Deposited Residue Count: 11,587
Unique protein chains: 28
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPD	A [auth 0]	778	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06839 Go to UniProtKB: P06839
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06839
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TFB1 isoform 1	B [auth 1]	642	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32776 Go to UniProtKB: P32776
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32776
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II transcription factor B subunit 2	C [auth 2]	513	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02939 Go to UniProtKB: Q02939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02939
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB4	D [auth 4]	338	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12004 Go to UniProtKB: Q12004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12004
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH	E [auth 6]	461	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04673 Go to UniProtKB: Q04673
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04673
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPB	F [auth 7]	843	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00578 Go to UniProtKB: Q00578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00578
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIB	G [auth M]	345	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SUA7, YPR086W, P9513.4
UniProt
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29055 Go to UniProtKB: P29055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29055
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	H [auth A]	1,733	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	I [auth B]	1,224	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08518
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	J [auth C]	318	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16370
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	K [auth D]	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433 Go to UniProtKB: P20433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20433
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	L [auth E]	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20434
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	M [auth F]	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20435
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	N [auth G]	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087 Go to UniProtKB: P34087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34087
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	O [auth H]	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20436
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	P [auth I]	122	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27999
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II subunit RPABC5	Q [auth J]	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22139
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	R [auth K]	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38902
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases II subunit RPABC4	S [auth L]	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40422
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit alpha	T [auth Q]	735	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41895 Go to UniProtKB: P41895
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41895
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit beta	U [auth P]	400	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41896 Go to UniProtKB: P41896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41896
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor	V [auth S]	309	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DST1
UniProt
Find proteins for P07273 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07273 Go to UniProtKB: P07273
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07273
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box-binding protein	W [auth O]	240	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPT15, BTF1, TBP1, YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393 Go to UniProtKB: P13393
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13393
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA large subunit	X [auth U]	286	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PACBIOSEQ_LOCUS5691, SCNYR20_0002031500, SCP684_0003030900
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32773 Go to UniProtKB: P32773
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32773
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA subunit 2	Y [auth V]	122	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PACBIOSEQ_LOCUS3356, PACBIOSEQ_LOCUS3547, PACBIOSEQ_LOCUS3591, PACBIOSEQ_LOCUS3602, PACBIOSEQ_LOCUS3607, PACBIOSEQ_LOCUS3639, PACBIOSEQ_LOCUS3680, PACBIOSEQ_LOCUS3892, PACBIOSEQ_LOCUS3963
UniProt
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32774 Go to UniProtKB: P32774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32774
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit alpha	Z [auth W]	482	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36100 Go to UniProtKB: P36100
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36100
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit beta	AA [auth X]	328	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36145 Go to UniProtKB: P36145
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36145
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB5	BA [auth 5]	72	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7C1 Go to UniProtKB: Q3E7C1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3E7C1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 29
DNA (64-MER)	CA [auth N]	64	Saccharomyces cerevisiae
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Molecule	Chains	Length	Organism
Entity ID: 30
DNA (64-MER)	DA [auth T]	64	Saccharomyces cerevisiae
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth 0] MOL2 format, chain EA [auth 0] mmCIF format, chain EA [auth 0]	EA [auth 0]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain EA [auth 0] Interactions & Density Focus chain EA [auth 0]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IA [auth 6] SDF format, chain PA [auth B] SDF format, chain RA [auth I] SDF format, chain VA [auth S] SDF format, chain UA [auth L] SDF format, chain TA [auth J] SDF format, chain SA [auth I] SDF format, chain QA [auth C] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth M] SDF format, chain JA [auth 6] SDF format, chain HA [auth 6] SDF format, chain GA [auth 6] SDF format, chain FA [auth 4] MOL2 format, chain IA [auth 6] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain VA [auth S] MOL2 format, chain UA [auth L] MOL2 format, chain TA [auth J] MOL2 format, chain SA [auth I] MOL2 format, chain QA [auth C] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth M] MOL2 format, chain JA [auth 6] MOL2 format, chain HA [auth 6] MOL2 format, chain GA [auth 6] MOL2 format, chain FA [auth 4] mmCIF format, chain IA [auth 6] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain VA [auth S] mmCIF format, chain UA [auth L] mmCIF format, chain TA [auth J] mmCIF format, chain SA [auth I] mmCIF format, chain QA [auth C] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth M] mmCIF format, chain JA [auth 6] mmCIF format, chain HA [auth 6] mmCIF format, chain GA [auth 6] mmCIF format, chain FA [auth 4]	FA [auth 4] GA [auth 6] HA [auth 6] IA [auth 6] JA [auth 6] FA [auth 4], GA [auth 6], HA [auth 6], IA [auth 6], JA [auth 6], LA [auth M], MA [auth A], NA [auth A], PA [auth B], QA [auth C], RA [auth I], SA [auth I], TA [auth J], UA [auth L], VA [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain FA [auth 4] Focus chain GA [auth 6] Focus chain HA [auth 6] Focus chain IA [auth 6] Focus chain JA [auth 6] Focus chain LA [auth M] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain TA [auth J] Focus chain UA [auth L] Focus chain VA [auth S] Interactions & Density Focus chain FA [auth 4] Focus chain GA [auth 6] Focus chain HA [auth 6] Focus chain IA [auth 6] Focus chain JA [auth 6] Focus chain LA [auth M] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain TA [auth J] Focus chain UA [auth L] Focus chain VA [auth S]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain KA [auth 7] SDF format, chain OA [auth A] MOL2 format, chain KA [auth 7] MOL2 format, chain OA [auth A] mmCIF format, chain KA [auth 7] mmCIF format, chain OA [auth A]	KA [auth 7], OA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain KA [auth 7] Focus chain OA [auth A] Interactions & Density Focus chain KA [auth 7] Focus chain OA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Yang, C.

Murakami, K.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8UMI | pdb_00008umi

consensus map of PICdeltaTFIIK form1

Literature

consensus map of PICdeltaTFIIK form1

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt