1RM1 | pdb_00001rm1

Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex

• PDB DOI: https://doi.org/10.2210/pdb1RM1/pdb
• NAKB: 1RM1

• Classification: TRANSCRIPTION/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-26 Released: 2005-07-26 
• Deposition Author(s): Jin, X., Gewirth, D.T., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

High Resolution Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex

Jin, X., Gewirth, D.T., Geiger, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.78 kDa 
• Atom Count: 4,200 
• Modeled Residue Count: 433 
• Deposited Residue Count: 684 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box binding protein	C [auth A]	240	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SPT15, BTF1, YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393  Go to UniProtKB:  P13393

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA small chain	D [auth B]	122	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TOA2, YKL058W
UniProt
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32774  Go to UniProtKB:  P32774

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA large chain	E [auth C]	286	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TOA1, YOR194C
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32773  Go to UniProtKB:  P32773

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*AP*TP*AP*AP*AP*AP*CP*G)-3'	A [auth D]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*CP*GP*TP*TP*TP*TP*AP*TP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3'	B [auth E]	18	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.25	α = 90
b = 173.25	β = 90
c = 164.07	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Jin, X., Gewirth, D.T., Geiger, J.H.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Refinement description