7TYS

Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to ATP and repaglinide with Kir6.2-CTD in the up conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6PZ9


Literature

Ligand-mediated Structural Dynamics of a Mammalian Pancreatic K ATP Channel.

Sung, M.W.Driggers, C.M.Mostofian, B.Russo, J.D.Patton, B.L.Zuckerman, D.M.Shyng, S.L.

(2022) J Mol Biol 434: 167789-167789

  • DOI: https://doi.org/10.1016/j.jmb.2022.167789
  • Primary Citation of Related Structures:  
    7TYS, 7TYT, 7U1E, 7U1Q, 7U1S, 7U24, 7U2X, 7U6Y, 7U7M, 7UAA, 7UQR

  • PubMed Abstract: 

    Regulation of pancreatic K ATP channels involves orchestrated interactions of their subunits, Kir6.2 and SUR1, and ligands. Previously we reported K ATP channel cryo-EM structures in the presence and absence of pharmacological inhibitors and ATP, focusing on the mechanisms by which inhibitors act as pharmacological chaperones of K ATP channels (Martin et al., 2019). Here we analyzed the same cryo-EM datasets with a focus on channel conformational dynamics to elucidate structural correlates pertinent to ligand interactions and channel gating. We found pharmacological inhibitors and ATP enrich a channel conformation in which the Kir6.2 cytoplasmic domain is closely associated with the transmembrane domain, while depleting one where the Kir6.2 cytoplasmic domain is extended away into the cytoplasm. This conformational change remodels a network of intra- and inter-subunit interactions as well as the ATP and PIP 2 binding pockets. The structures resolved key contacts between the distal N-terminus of Kir6.2 and SUR1's ABC module involving residues implicated in channel function and showed a SUR1 residue, K134, participates in PIP 2 binding. Molecular dynamics simulations revealed two Kir6.2 residues, K39 and R54, that mediate both ATP and PIP 2 binding, suggesting a mechanism for competitive gating by ATP and PIP 2 .


  • Organizational Affiliation

    Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA. Electronic address: https://twitter.com/MinWooSung5.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-sensitive inward rectifier potassium channel 11
A, B, C, D
390Rattus norvegicusMutation(s): 0 
Gene Names: Kcnj11
Membrane Entity: Yes 
UniProt
Find proteins for P70673 (Rattus norvegicus)
Explore P70673 
Go to UniProtKB:  P70673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70673
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-binding cassette sub-family C member 81,582Cricetus cricetusMutation(s): 0 
Gene Names: ABCC8SUR
Membrane Entity: Yes 
UniProt
Find proteins for Q09427 (Cricetus cricetus)
Explore Q09427 
Go to UniProtKB:  Q09427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09427
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S
Query on P5S

Download Ideal Coordinates CCD File 
BA [auth E]
K [auth A]
L [auth A]
O [auth B]
R [auth C]
BA [auth E],
K [auth A],
L [auth A],
O [auth B],
R [auth C],
T [auth D]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
POV
Query on POV

Download Ideal Coordinates CCD File 
CA [auth E],
J [auth A],
N [auth B],
Q [auth C],
U [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
P [auth C],
S [auth D],
X [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
65I
Query on 65I

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth E]
EA [auth E]
V [auth E]
Y [auth E]
AA [auth E],
DA [auth E],
EA [auth E],
V [auth E],
Y [auth E],
Z [auth E]
(9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate
C22 H44 N O8 P
WTEUZJKVOKXZKR-HXUWFJFHSA-N
BJX (Subject of Investigation/LOI)
Query on BJX

Download Ideal Coordinates CCD File 
W [auth E]Repaglinide
C27 H36 N2 O4
FAEKWTJYAYMJKF-QHCPKHFHSA-N
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01 DK066485-13 (PI: Shyng)

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references