6AUI

Human ribonucleotide reductase large subunit (alpha) with dATP and CDP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

3.3- angstrom resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound.

Brignole, E.J.Tsai, K.L.Chittuluru, J.Li, H.Aye, Y.Penczek, P.A.Stubbe, J.Drennan, C.L.Asturias, F.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.31502
  • Primary Citation of Related Structures:  
    6AUI

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides, a reaction essential for DNA replication and repair. Human RNR requires two subunits for activity, the α subunit contains the active site, and the β subunit houses the radical cofactor. Here, we present a 3.3-Å resolution structure by cryo-electron microscopy (EM) of a dATP-inhibited state of human RNR. This structure, which was determined in the presence of substrate CDP and allosteric regulators ATP and dATP, has three α 2 units arranged in an α 6 ring. At near-atomic resolution, these data provide insight into the molecular basis for CDP recognition by allosteric specificity effectors dATP/ATP. Additionally, we present lower-resolution EM structures of human α 6 in the presence of both the anticancer drug clofarabine triphosphate and β 2 . Together, these structures support a model for RNR inhibition in which β 2 is excluded from binding in a radical transfer competent position when α exists as a stable hexamer.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase large subunit
A, B, C, D, E
A, B, C, D, E, F
812Homo sapiensMutation(s): 0 
Gene Names: RRM1RR1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23921
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth E]
FA [auth F]
G [auth A]
HA [auth F]
AA [auth E],
CA [auth E],
FA [auth F],
G [auth A],
HA [auth F],
I [auth A],
L [auth B],
N [auth B],
Q [auth C],
S [auth C],
V [auth D],
X [auth D]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
CDP
Query on CDP

Download Ideal Coordinates CCD File 
EA [auth E]
JA [auth F]
K [auth A]
P [auth B]
U [auth C]
EA [auth E],
JA [auth F],
K [auth A],
P [auth B],
U [auth C],
Z [auth D]
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
DA [auth E]
GA [auth F]
H [auth A]
IA [auth F]
BA [auth E],
DA [auth E],
GA [auth F],
H [auth A],
IA [auth F],
J [auth A],
M [auth B],
O [auth B],
R [auth C],
T [auth C],
W [auth D],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29595
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM67167

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations