8UMH | pdb_00008umh

Consensus map of PICdeltaTFIIK form2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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

consensus map of PICdeltaTFIIK form2

Yang, C., Murakami, K.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBA [auth M]345Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUA7, YPR086W, P9513.4
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitB [auth A]1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth B]1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3D [auth C]318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3G [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9H [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II subunit RPABC5I [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11J [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II subunit RPABC4K [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaL [auth Q]735Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit betaM [auth P]400Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factorN [auth S]309Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding protein240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15, BTF1, TBP1, YER148W
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunitP [auth U]286Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5691, SCNYR20_0002031500, SCP684_0003030900
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2Q [auth V]122Saccharomyces cerevisiaeMutation(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))
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UniProt GroupP32774
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alphaR [auth W]482Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP36100
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaS [auth X]328Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4T [auth D]221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7U [auth G]171Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP34087
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPDV [auth 0]778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
TFB1 isoform 1W [auth 1]642Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB4X [auth 4]338Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIHY [auth 6]461Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBZ [auth 7]843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 2AA [auth 2]513Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH subunit TFB5BA [auth 5]72Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChains LengthOrganismImage
DNA (63-MER)CA [auth N]64Saccharomyces cerevisiae
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Entity ID: 30
MoleculeChains LengthOrganismImage
DNA (63-MER)DA [auth T]64Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
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PA [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EA [auth M]
FA [auth A]
GA [auth A]
IA [auth B]
JA [auth C]
EA [auth M],
FA [auth A],
GA [auth A],
IA [auth B],
JA [auth C],
KA [auth I],
LA [auth I],
MA [auth J],
NA [auth L],
OA [auth S],
QA [auth 4],
RA [auth 6],
SA [auth 6],
TA [auth 6],
UA [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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HA [auth A],
VA [auth 7]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant 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
  • Version 1.2: 2025-05-14
    Changes: Data collection