8BM0

Structure of GroEL:GroES-ATP complex plunge frozen 200 ms after reaction initiation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting.

Torino, S.Dhurandhar, M.Stroobants, A.Claessens, R.Efremov, R.G.

(2023) Nat Methods 20: 1400-1408

  • DOI: https://doi.org/10.1038/s41592-023-01967-z
  • Primary Citation of Related Structures:  
    8BK7, 8BK8, 8BK9, 8BKA, 8BKB, 8BKG, 8BKZ, 8BL2, 8BL7, 8BLC, 8BLD, 8BLE, 8BLF, 8BLY, 8BM0, 8BM1, 8BMD, 8BMO, 8BMT

  • PubMed Abstract: 

    Single-particle cryogenic electron microscopy (cryo-EM) allows reconstruction of high-resolution structures of proteins in different conformations. Protein function often involves transient functional conformations, which can be resolved using time-resolved cryo-EM (trEM). In trEM, reactions are arrested after a defined delay time by rapid vitrification of protein solution on the EM grid. Despite the increasing interest in trEM among the cryo-EM community, making trEM samples with a time resolution below 100 ms remains challenging. Here we report the design and the realization of a time-resolved cryo-plunger that combines a droplet-based microfluidic mixer with a laser-induced generator of microjets that allows rapid reaction initiation and plunge-freezing of cryo-EM grids. Using this approach, a time resolution of 5 ms was achieved and the protein density map was reconstructed to a resolution of 2.1 Å. trEM experiments on GroEL:GroES chaperonin complex resolved the kinetics of the complex formation and visualized putative short-lived conformations of GroEL-ATP complex.


  • Organizational Affiliation

    Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperonin GroEL548Escherichia coliMutation(s): 0 
Gene Names: groELgroLmopAb4143JW4103
EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Co-chaperonin GroES98Escherichia coliMutation(s): 0 
Gene Names: groESgroSmopBb4142JW4102
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12))
Explore P0A6F9 
Go to UniProtKB:  P0A6F9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BB [auth O]
DA [auth A]
DB [auth Q]
FA [auth C]
HB [auth R]
BB [auth O],
DA [auth A],
DB [auth Q],
FA [auth C],
HB [auth R],
JA [auth D],
JB [auth T],
LA [auth F],
PA [auth H],
RA [auth K],
VA [auth L],
X [auth I],
XA [auth N],
Z [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth G]
AB [auth O]
CA [auth A]
EB [auth Q]
GA [auth C]
AA [auth G],
AB [auth O],
CA [auth A],
EB [auth Q],
GA [auth C],
GB [auth R],
IA [auth D],
KB [auth T],
MA [auth F],
OA [auth H],
SA [auth K],
UA [auth L],
W [auth I],
YA [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth A]
CB [auth Q]
EA [auth C]
FB [auth R]
HA [auth D]
BA [auth A],
CB [auth Q],
EA [auth C],
FB [auth R],
HA [auth D],
IB [auth T],
KA [auth F],
NA [auth H],
QA [auth K],
TA [auth L],
V [auth I],
WA [auth N],
Y [auth G],
ZA [auth O]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union726436
Research Foundation - Flanders (FWO)BelgiumG0H5916N
Research Foundation - Flanders (FWO)BelgiumG054617N

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-13
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Database references