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PDBsum entry 5iy7
Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Transcription, transferase/DNA PDB id
5iy7

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
1454 a.a.
1165 a.a.
275 a.a.
129 a.a.
210 a.a.
86 a.a.
171 a.a.
150 a.a.
125 a.a.
67 a.a.
117 a.a.
46 a.a.
310 a.a.
113 a.a.
99 a.a.
185 a.a.
180 a.a.
165 a.a.
138 a.a.
222 a.a.
170 a.a.
475 a.a.
665 a.a.
188 a.a.
62 a.a.
274 a.a.
193 a.a.
DNA/RNA
Metals
_ZN ×11
_MG ×2
PDB id:
5iy7
Name: Transcription, transferase/DNA
Title: Human holo-pic in the open state
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1, DNA-directed RNA polymerase ii subunit a, DNA-directed RNA polymerase iii largest subunit, RNA- directed RNA polymerase ii subunit rpb1. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: DNA-directed RNA polymerase ii 140 kda polypeptide, DNA- directed RNA polymerase ii subunit b, RNA polymerase ii subunit 2,
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gtf2b, tf2b, tfiib. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gtf2a1, tf2a1. Gene: gtf2a2, tf2a2. Gene: tbp, gtf2d1, tf2d, tfiid.
Authors: Y.He,C.Yan,J.Fang,C.Inouye,R.Tjian,I.Ivanov,E.Nogales
Key ref: Y.He et al. (2016). Near-atomic resolution visualization of human transcription promoter opening. Nature, 533, 359-365. PubMed id: 27193682 DOI: 10.1038/nature17970
Date:
24-Mar-16     Release date:   18-May-16    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24928  (RPB1_HUMAN) -  DNA-directed RNA polymerase II subunit RPB1 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1970 a.a.
1454 a.a.
Protein chain
Pfam   ArchSchema ?
P30876  (RPB2_HUMAN) -  DNA-directed RNA polymerase II subunit RPB2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1174 a.a.
1165 a.a.
Protein chain
Pfam   ArchSchema ?
P19387  (RPB3_HUMAN) -  DNA-directed RNA polymerase II subunit RPB3 from Homo sapiens
Seq:
Struc: 		275 a.a.
275 a.a.
Protein chain
Pfam   ArchSchema ?
O15514  (RPB4_HUMAN) -  DNA-directed RNA polymerase II subunit RPB4 from Homo sapiens
Seq:
Struc: 		142 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P19388  (RPAB1_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Homo sapiens
Seq:
Struc: 		210 a.a.
210 a.a.
Protein chain
Pfam   ArchSchema ?
P61218  (RPAB2_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Homo sapiens
Seq:
Struc: 		127 a.a.
86 a.a.
Protein chain
Pfam   ArchSchema ?
P62487  (RPB7_HUMAN) -  DNA-directed RNA polymerase II subunit RPB7 from Homo sapiens
Seq:
Struc: 		172 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P52434  (RPAB3_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Homo sapiens
Seq:
Struc: 		150 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P36954  (RPB9_HUMAN) -  DNA-directed RNA polymerase II subunit RPB9 from Homo sapiens
Seq:
Struc: 		125 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P62875  (RPAB5_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Homo sapiens
Seq:
Struc: 		67 a.a.
67 a.a.
Protein chain
Pfam   ArchSchema ?
P52435  (RPB11_HUMAN) -  DNA-directed RNA polymerase II subunit RPB11-a from Homo sapiens
Seq:
Struc: 		117 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P53803  (RPAB4_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Homo sapiens
Seq:
Struc: 		58 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
Q00403  (TF2B_HUMAN) -  Transcription initiation factor IIB from Homo sapiens
Seq:
Struc: 		316 a.a.
310 a.a.
Protein chain
Pfam   ArchSchema ?
P52655  (TF2AA_HUMAN) -  Transcription initiation factor IIA subunit 1 from Homo sapiens
Seq:
Struc: 		376 a.a.
113 a.a.*
Protein chain
Pfam   ArchSchema ?
P52657  (T2AG_HUMAN) -  Transcription initiation factor IIA subunit 2 from Homo sapiens
Seq:
Struc: 		109 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P20226  (TBP_HUMAN) -  TATA-box-binding protein from Homo sapiens
Seq:
Struc: 		339 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P29083  (T2EA_HUMAN) -  General transcription factor IIE subunit 1 from Homo sapiens
Seq:
Struc: 		439 a.a.
180 a.a.
Protein chain
Pfam   ArchSchema ?
P29084  (T2EB_HUMAN) -  Transcription initiation factor IIE subunit beta from Homo sapiens
Seq:
Struc: 		291 a.a.
165 a.a.
Protein chain
Pfam   ArchSchema ?
P35269  (T2FA_HUMAN) -  General transcription factor IIF subunit 1 from Homo sapiens
Seq:
Struc: 		517 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P13984  (T2FB_HUMAN) -  General transcription factor IIF subunit 2 from Homo sapiens
Seq:
Struc: 		249 a.a.
222 a.a.
Protein chain
Pfam   ArchSchema ?
P23193  (TCEA1_HUMAN) -  Transcription elongation factor A protein 1 from Homo sapiens
Seq:
Struc: 		301 a.a.
170 a.a.
Protein chain
Pfam   ArchSchema ?
P19447  (ERCC3_HUMAN) -  General transcription and DNA repair factor IIH helicase/translocase subunit XPB from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		782 a.a.
475 a.a.
Protein chain
Pfam   ArchSchema ?
P18074  (ERCC2_HUMAN) -  General transcription and DNA repair factor IIH helicase subunit XPD from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		760 a.a.
665 a.a.
Protein chain
Pfam   ArchSchema ?
Q13888  (TF2H2_HUMAN) -  General transcription factor IIH subunit 2 from Homo sapiens
Seq:
Struc: 		395 a.a.
188 a.a.
Protein chain
Pfam   ArchSchema ?
Q6ZYL4  (TF2H5_HUMAN) -  General transcription factor IIH subunit 5 from Homo sapiens
Seq:
Struc: 		71 a.a.
62 a.a.
Protein chain
Pfam   ArchSchema ?
Q92759  (TF2H4_HUMAN) -  General transcription factor IIH subunit 4 from Homo sapiens
Seq:
Struc: 		462 a.a.
274 a.a.
Protein chain
Pfam   ArchSchema ?
Q13889  (TF2H3_HUMAN) -  General transcription factor IIH subunit 3 from Homo sapiens
Seq:
Struc: 		308 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 40 residue positions (black crosses)

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

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.2.7.7.48  - RNA-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 2: 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 3: Chains A, B: E.C.3.1.13.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 4: Chain M: 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 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(+)
   Enzyme class 6: Chain V: E.C.5.6.2.4  - Dna 3'-5' helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 7: Chain W: E.C.5.6.2.3  - Dna 5'-3' helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
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    
 
 
DOI no: 10.1038/nature17970 Nature 533:359-365 (2016)
PubMed id: 27193682  
 
 
Near-atomic resolution visualization of human transcription promoter opening.
Y.He, C.Yan, J.Fang, C.Inouye, R.Tjian, I.Ivanov, E.Nogales.
 
  ABSTRACT  
 
In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.
 

 

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