1J2X | pdb_00001j2x

Crystal structure of RAP74 C-terminal domain complexed with FCP1 C-terminal peptide

• PDB DOI: https://doi.org/10.2210/pdb1J2X/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-15 Released: 2003-01-30 
• Deposition Author(s): Kamada, K., Roeder, R.G., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism of recruitment of TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF

Kamada, K., Roeder, R.G., Burley, S.K.

(2003) Proc Natl Acad Sci U S A 100: 2296-2299

• PubMed: 12591941 
• DOI: https://doi.org/10.1073/pnas.262798199
• Primary Citation Related Structures: 
  1J2X


• PubMed Abstract: 
  

  After mRNA transcription termination in eukaryotes, the hyperphosphorylated form of RNA polymerase II (pol II0) must be recycled by TFIIF-associating C-terminal domain phosphatase (FCP1), the phosphatase responsible for dephosphorylating the C-terminal domain of the largest polymerase subunit. Transcription factor (TF)-IIF stimulates the activity of FCP1, and the RNA polymerase II-associating protein 74 subunit of TFIIF forms a complex with FCP1 in both human and yeast. Here, we report a cocrystal structure of the winged-helix domain of human RNA polymerase II-associating protein 74 bound to the alpha-helical C terminus of human FCP1 (residues 944-961). These results illustrate the molecular mechanism by which TFIIF efficiently recruits FCP1 to the pol II transcription machinery for recycling of the polymerase.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.61 kDa 
• Atom Count: 774 
• Modeled Residue Count: 88 
• Deposited Residue Count: 91 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF, alpha subunit	A	73	Homo sapiens	Mutation(s): 0  Gene Names: RAP74
UniProt & NIH Common Fund Data Resources
Find proteins for P35269 (Homo sapiens) Explore P35269  Go to UniProtKB:  P35269
GTEx:  ENSG00000125651

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II CTD phosphatase	B	18	N/A	Mutation(s): 0  EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5B0 (Homo sapiens) Explore Q9Y5B0  Go to UniProtKB:  Q9Y5B0
PHAROS:  Q9Y5B0 GTEx:  ENSG00000060069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.605	α = 90
b = 30.446	β = 106.38
c = 47.379	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-30 
Deposition Author(s): Kamada, K., Roeder, R.G., Burley, S.K.

Revision History  

• Version 1.0: 2003-01-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description