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PDBsum entry 7edx
Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Transcription PDB id
7edx

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
602 a.a.
963 a.a.
165 a.a.
546 a.a.
404 a.a.
145 a.a.
209 a.a.
120 a.a.
89 a.a.
76 a.a.
97 a.a.
177 a.a.
122 a.a.
248 a.a.
134 a.a.
113 a.a.
127 a.a.
158 a.a.
95 a.a.
98 a.a.
107 a.a.
87 a.a.
1427 a.a.
1134 a.a.
257 a.a.
128 a.a.
209 a.a.
79 a.a.
148 a.a.
114 a.a.
64 a.a.
117 a.a.
44 a.a.
171 a.a.
DNA/RNA
Metals
_ZN ×9
_MG
PDB id:
7edx
Name: Transcription
Title: P53-bound tfiid-based core pic on hdm2 promoter
Structure: Transcription initiation factor tfiid subunit 1. Chain: a. Synonym: cell cycle gene 1 protein,tbp-associated factor 250 kda, p250,transcription initiation factor tfiid 250 kda subunit,taf(ii) 250,tafii-250,tafii250. Engineered: yes. Transcription initiation factor tfiid subunit 2. Chain: b. Synonym: 150 kda cofactor of initiator function,RNA polymerase ii
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: taf1, ba2r, ccg1, ccgs, taf2a. Expressed in: homo sapiens. Expression_system_taxid: 9606. Gene: taf2, cif150, taf2b. Gene: taf4, taf2c, taf2c1, taf4a, tafii130, tafii135. Gene: taf5, taf2d.
Authors: X.Chen,Y.Qi,H.Hou,X.Wang,Z.Wu,J.Li,Y.Xu
Key ref: X.Chen et al. Structural insights into preinitiation complex assemb core promoters.. Science, . PubMed id: 33795473
Date:
17-Mar-21     Release date:   05-May-21    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21675  (TAF1_HUMAN) -  Transcription initiation factor TFIID subunit 1 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1893 a.a.
602 a.a.
Protein chain
Pfam   ArchSchema ?
Q6P1X5  (TAF2_HUMAN) -  Transcription initiation factor TFIID subunit 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1199 a.a.
963 a.a.
Protein chain
Pfam   ArchSchema ?
O00268  (TAF4_HUMAN) -  Transcription initiation factor TFIID subunit 4 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1085 a.a.
165 a.a.
Protein chains
Pfam   ArchSchema ?
Q15542  (TAF5_HUMAN) -  Transcription initiation factor TFIID subunit 5 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		800 a.a.
546 a.a.
Protein chains
Pfam   ArchSchema ?
P49848  (TAF6_HUMAN) -  Transcription initiation factor TFIID subunit 6 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		677 a.a.
404 a.a.
Protein chain
Pfam   ArchSchema ?
Q15545  (TAF7_HUMAN) -  Transcription initiation factor TFIID subunit 7 from Homo sapiens
Seq:
Struc: 		349 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
Q7Z7C8  (TAF8_HUMAN) -  Transcription initiation factor TFIID subunit 8 from Homo sapiens
Seq:
Struc: 		310 a.a.
209 a.a.
Protein chains
Pfam   ArchSchema ?
Q16594  (TAF9_HUMAN) -  Transcription initiation factor TFIID subunit 9 from Homo sapiens
Seq:
Struc: 		264 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
Q12962  (TAF10_HUMAN) -  Transcription initiation factor TFIID subunit 10 from Homo sapiens
Seq:
Struc: 		218 a.a.
89 a.a.
Protein chain
Pfam   ArchSchema ?
Q16514  (TAF12_HUMAN) -  Transcription initiation factor TFIID subunit 12 from Homo sapiens
Seq:
Struc: 		161 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P52657  (T2AG_HUMAN) -  Transcription initiation factor IIA subunit 2 from Homo sapiens
Seq:
Struc: 		109 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P20226  (TBP_HUMAN) -  TATA-box-binding protein from Homo sapiens
Seq:
Struc: 		339 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P52655  (TF2AA_HUMAN) -  Transcription initiation factor IIA subunit 1 from Homo sapiens
Seq:
Struc: 		376 a.a.
122 a.a.*
Protein chain
Pfam   ArchSchema ?
Q00403  (TF2B_HUMAN) -  Transcription initiation factor IIB from Homo sapiens
Seq:
Struc: 		316 a.a.
248 a.a.
Protein chain
Pfam   ArchSchema ?
P35269  (T2FA_HUMAN) -  General transcription factor IIF subunit 1 from Homo sapiens
Seq:
Struc: 		517 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
P13984  (T2FB_HUMAN) -  General transcription factor IIF subunit 2 from Homo sapiens
Seq:
Struc: 		249 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q5VWG9  (TAF3_HUMAN) -  Transcription initiation factor TFIID subunit 3 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		929 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
O00268  (TAF4_HUMAN) -  Transcription initiation factor TFIID subunit 4 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1085 a.a.
158 a.a.
Protein chain
Pfam   ArchSchema ?
Q12962  (TAF10_HUMAN) -  Transcription initiation factor TFIID subunit 10 from Homo sapiens
Seq:
Struc: 		218 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
Q15544  (TAF11_HUMAN) -  Transcription initiation factor TFIID subunit 11 from Homo sapiens
Seq:
Struc: 		211 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
Q16514  (TAF12_HUMAN) -  Transcription initiation factor TFIID subunit 12 from Homo sapiens
Seq:
Struc: 		161 a.a.
107 a.a.
Protein chain
Pfam   ArchSchema ?
Q15543  (TAF13_HUMAN) -  Transcription initiation factor TFIID subunit 13 from Homo sapiens
Seq:
Struc: 		124 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
A0A7M4DUC2  (A0A7M4DUC2_PIG) -  DNA-directed RNA polymerase subunit from Sus scrofa
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1984 a.a.
1427 a.a.
Protein chain
Pfam   ArchSchema ?
I3LGP4  (I3LGP4_PIG) -  DNA-directed RNA polymerase subunit beta from Sus scrofa
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1300 a.a.
1134 a.a.
Protein chain
Pfam   ArchSchema ?
I3LCH3  (I3LCH3_PIG) -  DNA-directed RNA polymerase II subunit RPB3 from Sus scrofa
Seq:
Struc: 		275 a.a.
257 a.a.
Protein chain
Pfam   ArchSchema ?
A0A287ADR4  (A0A287ADR4_PIG) -  RNA polymerase II subunit D from Sus scrofa
Seq:
Struc: 		184 a.a.
128 a.a.
Protein chain
Pfam   ArchSchema ?
I3LSI7  (I3LSI7_PIG) -  DNA-directed RNA polymerase II subunit E from Sus scrofa
Seq:
Struc: 		210 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
A0A4X1VEK9  (A0A4X1VEK9_PIG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Sus scrofa
Seq:
Struc: 		127 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
I3LCB2  (I3LCB2_PIG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Sus scrofa
Seq:
Struc: 		150 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
P60899  (RPB9_PIG) -  DNA-directed RNA polymerase II subunit RPB9 from Sus scrofa
Seq:
Struc: 		125 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
A0A4X1VYD0  (A0A4X1VYD0_PIG) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Sus scrofa
Seq:
Struc: 		67 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
F1RKE4  (F1RKE4_PIG) -  DNA-directed RNA polymerase II subunit RPB11-a from Sus scrofa
Seq:
Struc: 		117 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
A0A4X1TRS6  (A0A4X1TRS6_PIG) -  RNA polymerase II, I and III subunit K from Sus scrofa
Seq:
Struc: 		58 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
A0A4X1VKG7  (A0A4X1VKG7_PIG) -  DNA-directed RNA polymerase subunit from Sus scrofa
Seq:
Struc: 		172 a.a.
171 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 48 residue positions (black crosses)

DNA/RNA chains
  T-C-T-C-C-A-G-C-T-G-G-G-G-C-T-A-T-T-T-A-A-A-C-C-A-T-G-C-A-T-T-T-T-C-C-C-A-G-C- 77 bases
  G-T-G-C-C-C-A-C-A-G-G-T-C-T-A-C-C-C-T-C-C-A-A-T-C-G-C-C-A-C-T-G-A-A-C-A-C-A-G- 77 bases

 Enzyme reactions 
   Enzyme class 2: Chains A, R: E.C.2.3.1.48  - histone acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-lysyl-[protein] + acetyl-CoA = N6-acetyl-L-lysyl-[protein] + CoA + H+
L-lysyl-[protein]
 + acetyl-CoA
 = N(6)-acetyl-L-lysyl-[protein]
 + CoA
 + H(+)
   Enzyme class 3: Chain A: E.C.2.7.11.1  - non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H+
2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H+
L-seryl-[protein]
 + ATP
 = O-phospho-L-seryl-[protein]
 + ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
 + ADP
 + H(+)
   Enzyme class 4: Chains o, p: 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 T: 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

 

 

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