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 6AUI | pdb_00006aui

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

Validation slider image for 6AUI

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 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.

Macromolecule Content 

  • Total Structure Weight: 562.71 kDa 
  • Atom Count: 36,306 
  • Modeled Residue Count: 4,470 
  • Deposited Residue Count: 4,872 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: RRM1, RR1
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
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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