Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 182.25 kDa 
• Atom Count: 11549 
• Modelled Residue Count: 1452 
• Deposited Residue Count: 1584 
• Unique protein chains: 1

3HNF

Crystal structure of human ribonucleotide reductase 1 bound to the effectors TTP and dATP

• DOI: 10.2210/pdb3HNF/pdb

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


• Deposited: 2009-05-31 Released: 2011-02-23 
• Deposition Author(s): Fairman, J.W., Wijerathna, S.R., Xu, H., Dealwis, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.260 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization.

Fairman, J.W., Wijerathna, S.R., Ahmad, M.F., Xu, H., Nakano, R., Jha, S., Prendergast, J., Welin, R.M., Flodin, S., Roos, A., Nordlund, P., Li, Z., Walz, T., Dealwis, C.G.

(2011) Nat Struct Mol Biol 18: 316-322

• PubMed: 21336276 
• DOI: 10.1038/nsmb.2007
• Primary Citation of Related Structures:  
  2WGH, 3HNC, 3HND, 3HNE, 3HNF, 3PAW


• PubMed Abstract: 
  

Ribonucleotide reductase (RR) is an α(n)β(n) (RR1-RR2) complex that maintains balanced dNTP pools by reducing NDPs to dNDPs. RR1 is the catalytic subunit, and RR2 houses the free radical required for catalysis. RR is allosterically regulated by its activator ATP and its inhibitor dATP, which regulate RR activity by inducing oligomerization of RR1. Here, we report the first X-ray structures of human RR1 bound to TTP alone, dATP alone, TTP-GDP, TTP-ATP, and TTP-dATP. These structures provide insights into regulation of RR by ATP or dATP. At physiological dATP concentrations, RR1 forms inactive hexamers. We determined the first X-ray structure of the RR1-dATP hexamer and used single-particle electron microscopy to visualize the α(6)-ββ'-dATP holocomplex. Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization.

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Organizational Affiliation: 

Department of Biochemistry, University of Tennessee, Knoxville, TN, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase large subunit	A, B	792	Homo sapiens	Mutation(s): 0  Gene Names: RR1, RRM1 EC: 1.17.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23921 (Homo sapiens) Explore P23921  Go to UniProtKB:  P23921
PHAROS:  P23921 GTEx:  ENSG00000167325

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP	I [auth B]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
TTP	D [auth A], H [auth B]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
SO4	E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.260 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.856	α = 90
b = 114.388	β = 90
c = 220.003	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-31 
• Released Date: 2011-02-23 
Deposition Author(s): Fairman, J.W., Wijerathna, S.R., Xu, H., Dealwis, C.G.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description