spacer
spacer

PDBsum entry 5oqj
Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transcription PDB id
5oqj

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
1398 a.a.
1152 a.a.
262 a.a.
157 a.a.
213 a.a.
83 a.a.
171 a.a.
136 a.a.
116 a.a.
65 a.a.
112 a.a.
45 a.a.
279 a.a.
180 a.a.
148 a.a.
190 a.a.
92 a.a.
100 a.a.
258 a.a.
160 a.a.
698 a.a.
491 a.a.
395 a.a.
138 a.a.
297 a.a.
66 a.a.
335 a.a.
408 a.a.
43 a.a.
DNA/RNA
Ligands
SF4
Metals
_MG
_ZN ×16
PDB id:
5oqj
Name: Transcription
Title: Structure of yeast transcription pre-initiation complex with tfiih
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1,DNA-directed RNA polymerase iii largest subunit,RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2,b150,DNA-directed RNA polymerase ii 140 kda polypeptide. DNA-directed RNA polymerase ii subunit rpb3.
Source: Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Gene: sua7, ypr086w, p9513.4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct.
Authors: S.Schilbach,M.Hantsche,D.Tegunov,C.Dienemann,C.Wigge,U.Henning, P.Cramer
Key ref: S.Schilbach et al. (2017). Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature, 551, 204-209. PubMed id: 29088706
Date:
11-Aug-17     Release date:   25-Apr-18    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1733 a.a.
1398 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1224 a.a.
1152 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		318 a.a.
262 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		221 a.a.
157 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		215 a.a.
213 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		146 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		122 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		120 a.a.
112 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
45 a.a.
Protein chain
Pfam   ArchSchema ?
P29055  (TF2B_YEAST) -  Transcription initiation factor IIB from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		345 a.a.
279 a.a.
Protein chain
Pfam   ArchSchema ?
P13393  (TBP_YEAST) -  TATA-box-binding protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		240 a.a.
180 a.a.
Protein chain
Pfam   ArchSchema ?
P41895  (T2FA_YEAST) -  Transcription initiation factor IIF subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		735 a.a.
148 a.a.*
Protein chain
Pfam   ArchSchema ?
P41896  (T2FB_YEAST) -  Transcription initiation factor IIF subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		400 a.a.
190 a.a.
Protein chain
Pfam   ArchSchema ?
P32773  (TOA1_YEAST) -  Transcription initiation factor IIA large subunit from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		286 a.a.
92 a.a.*
Protein chain
Pfam   ArchSchema ?
P32774  (T2AG_YEAST) -  Transcription initiation factor IIA subunit 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		122 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P36100  (T2EA_YEAST) -  Transcription initiation factor IIE subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		482 a.a.
258 a.a.*
Protein chain
Pfam   ArchSchema ?
P36145  (T2EB_YEAST) -  Transcription initiation factor IIE subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		328 a.a.
160 a.a.
Protein chain
Pfam   ArchSchema ?
P06839  (RAD3_YEAST) -  General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		778 a.a.
698 a.a.*
Protein chain
Pfam   ArchSchema ?
P32776  (TFB1_YEAST) -  General transcription and DNA repair factor IIH subunit TFB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		642 a.a.
491 a.a.*
Protein chain
Pfam   ArchSchema ?
Q02939  (TFB2_YEAST) -  General transcription and DNA repair factor IIH subunit TFB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		513 a.a.
395 a.a.*
Protein chain
Pfam   ArchSchema ?
Q03290  (TFB3_YEAST) -  RNA polymerase II transcription factor B subunit 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		321 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q12004  (TFB4_YEAST) -  General transcription and DNA repair factor IIH subunit TFB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		338 a.a.
297 a.a.*
Protein chain
Pfam   ArchSchema ?
Q3E7C1  (TFB5_YEAST) -  General transcription and DNA repair factor IIH subunit TFB5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		72 a.a.
66 a.a.
Protein chain
Pfam   ArchSchema ?
Q04673  (SSL1_YEAST) -  General transcription and DNA repair factor IIH subunit SSL1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		461 a.a.
335 a.a.*
Protein chain
Pfam   ArchSchema ?
Q00578  (RAD25_YEAST) -  General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		843 a.a.
408 a.a.*
Protein chain
No UniProt id for this chain
Struc: 43 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 607 residue positions (black crosses)

DNA/RNA chains
  T-A-G-C-A-C-G-C-T-G-T-G-T-A-T-A-T-A-A-T-A-G-C-T-A-T-G-G-A-A-C-G-T-T-C-G-C-C-G- 76 bases
  T-T-G-T-G-C-T-A-T-G-A-T-A-T-T-T-T-T-A-T-G-T-A-T-G-T-A-C-A-A-C-A-C-A-C-A-T-C-G- 72 bases

 Enzyme reactions 
   Enzyme class 2: Chain 0: E.C.5.6.2.3  - Dna 5'-3' helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: Chain 7: E.C.5.6.2.4  - Dna 3'-5' helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 4: Chains A, B: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
 + diphosphate
   Enzyme class 5: Chain R: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nature 551:204-209 (2017)
PubMed id: 29088706  
 
 
Structures of transcription pre-initiation complex with TFIIH and Mediator.
S.Schilbach, M.Hantsche, D.Tegunov, C.Dienemann, C.Wigge, H.Urlaub, P.Cramer.
 
  ABSTRACT  
 
For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.
 

 

spacer
spacer