6CO7

Structure of the nvTRPM2 channel in complex with Ca2+

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structure of a TRPM2 channel in complex with Ca2+explains unique gating regulation.

Zhang, Z., Toth, B., Szollosi, A., Chen, J., Csanady, L.

(2018) Elife 7

  • DOI: 10.7554/eLife.36409
  • Primary Citation of Related Structures:  
    6CO7

  • PubMed Abstract: 

    • Transient receptor potential melastatin 2 (TRPM2) is a Ca 2+ -permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca 2+ , phosphatidyl-inositol-4,5-bisphosphate and ADP ribose ...

    Transient receptor potential melastatin 2 (TRPM2) is a Ca 2+ -permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca 2+ , phosphatidyl-inositol-4,5-bisphosphate and ADP ribose. Here, we present the ~3 Å resolution electron cryo-microscopic structure of TRPM2 from Nematostella vectensis , 63% similar in sequence to human TRPM2, in the Ca 2+ -bound closed state. Compared to other TRPM channels, TRPM2 exhibits unique structural features that correlate with its function. The pore is larger and more negatively charged, consistent with its high Ca 2+ selectivity and larger conductance. The intracellular Ca 2+ binding sites are connected to the pore and cytosol, explaining the unusual dependence of TRPM2 activity on intra- and extracellular Ca 2+ . In addition, the absence of a post-filter motif is likely the cause of the rapid inactivation of human TRPM2. Together, our cryo-EM and electrophysiology studies provide a molecular understanding of the unique gating mechanism of TRPM2.

    Organizational Affiliation: 

    MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted proteinA, B, C, D1560Nematostella vectensisMutation(s): 0 
Gene Names: v1g248535, TRPM2
Membrane Entity: Yes 
UniProt
Find proteins for A7T1N0 (Nematostella vectensis)
Explore A7T1N0 
Go to UniProtKB:  A7T1N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7T1N0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV
Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth C],
BA [auth B],
BB [auth C],
DA [auth B],
AA [auth A],
AB [auth C],
BA [auth B],
BB [auth C],
DA [auth B],
DB [auth C],
EA [auth B],
EB [auth C],
FA [auth B],
FB [auth C],
GA [auth B],
GB [auth C],
HA [auth B],
HB [auth D],
IA [auth B],
IB [auth D],
J [auth A],
JA [auth B],
JB [auth D],
K [auth A],
KA [auth B],
KB [auth D],
L [auth A],
LA [auth B],
LB [auth D],
M [auth A],
N [auth A],
NA [auth B],
NB [auth D],
O [auth A],
OA [auth B],
OB [auth D],
P [auth A],
PA [auth B],
PB [auth D],
Q [auth A],
QA [auth B],
QB [auth D],
R [auth A],
RA [auth C],
RB [auth D],
SB [auth D],
TA [auth C],
TB [auth D],
UA [auth C],
UB [auth D],
VA [auth C],
VB [auth D],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A],
ZA [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N		 Ligand Interaction
CLR
Query on CLR
Download Ideal Coordinates CCD File 
CA [auth B],
I [auth A],
MB [auth D],
SA [auth C]		CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
CB [auth C],
MA [auth B],
S [auth A],
WB [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
T [auth A],
U [auth A],
V [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The Rockefeller UniversityUnited States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary