6KPH

343 K cryoEM structure of Sso-KARI in complex with Mg2+, NADH and CPD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Temperature-Resolved Cryo-EM Uncovers Structural Bases of Temperature-Dependent Enzyme Functions.

Chen, C.Y.Chang, Y.C.Lin, B.L.Huang, C.H.Tsai, M.D.

(2019) J Am Chem Soc 141: 19983-19987

  • DOI: https://doi.org/10.1021/jacs.9b10687
  • Primary Citation of Related Structures:  
    6KOU, 6KPA, 6KPE, 6KPH, 6KPI, 6KPJ, 6KPK, 6KQ4, 6KQ8, 6KQJ, 6KQK, 6KQO

  • PubMed Abstract: 

    Protein functions are temperature-dependent, but protein structures are usually solved at a single (often low) temperature because of limitations on the conditions of crystal growth or protein vitrification. Here we demonstrate the feasibility of solving cryo-EM structures of proteins vitrified at high temperatures, solve 12 structures of an archaeal ketol-acid reductoisomerase (KARI) vitrified at 4-70 °C, and show that structures of both the Mg 2+ form (KARI:2Mg 2+ ) and its ternary complex (KARI:2Mg 2+ :NADH:inhibitor) are temperature-dependent in correlation with the temperature dependence of enzyme activity. Furthermore, structural analyses led to dissection of the induced-fit mechanism into ligand-induced and temperature-induced effects and to capture of temperature-resolved intermediates of the temperature-induced conformational change. The results also suggest that it is preferable to solve cryo-EM structures of protein complexes at functional temperatures. These studies should greatly expand the landscapes of protein structure-function relationships and enhance the mechanistic analysis of enzymatic functions.


  • Organizational Affiliation

    Department of Life Sciences , National Central University , Taoyuan 32001 , Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketol-acid reductoisomerase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
333Saccharolobus solfataricusMutation(s): 0 
Gene Names: SSOP1_1436
EC: 1.1.1.86
UniProt
Find proteins for Q97YJ9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97YJ9 
Go to UniProtKB:  Q97YJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97YJ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
AA [auth D]
CB [auth K]
EA [auth E]
GB [auth L]
IA [auth F]
AA [auth D],
CB [auth K],
EA [auth E],
GB [auth L],
IA [auth F],
MA [auth G],
O [auth A],
QA [auth H],
S [auth B],
UA [auth I],
W [auth C],
YA [auth J]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
9TY (Subject of Investigation/LOI)
Query on 9TY

Download Ideal Coordinates CCD File 
BA [auth D]
DB [auth K]
FA [auth E]
HB [auth L]
JA [auth F]
BA [auth D],
DB [auth K],
FA [auth E],
HB [auth L],
JA [auth F],
NA [auth G],
P [auth A],
RA [auth H],
T [auth B],
VA [auth I],
X [auth C],
ZA [auth J]
cyclopropane-1,1-dicarboxylic acid
C5 H6 O4
FDKLLWKMYAMLIF-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
BB [auth K]
CA [auth E]
DA [auth E]
EB [auth L]
AB [auth K],
BB [auth K],
CA [auth E],
DA [auth E],
EB [auth L],
FB [auth L],
GA [auth F],
HA [auth F],
KA [auth G],
LA [auth G],
M [auth A],
N [auth A],
OA [auth H],
PA [auth H],
Q [auth B],
R [auth B],
SA [auth I],
TA [auth I],
U [auth C],
V [auth C],
WA [auth J],
XA [auth J],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations