6CO7

Structure of the nvTRPM2 channel in complex with Ca2+

PDB DOI: https://doi.org/10.2210/pdb6CO7/pdb
EM Map EMD-7542: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Nematostella vectensis
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2018-03-12 Released: 2018-05-16
Deposition Author(s): Zhang, Z., Toth, B., Szollosi, A., Chen, J., Csanady, L.
Funding Organization(s): The Rockefeller University, Howard Hughes Medical Institute (HHMI)

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.

Macromolecule Content

Total Structure Weight: 752.69 kDa
Atom Count: 35,255
Modelled Residue Count: 4,244
Deposited Residue Count: 6,240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted protein	A, B, C, D	1,560	Nematostella vectensis	Mutation(s): 0 Gene Names: v1g248535 Membrane Entity: Yes
UniProt
Find proteins for A7T1N0 (Nematostella vectensis) Explore A7T1N0 Go to UniProtKB: A7T1N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7T1N0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain RB [auth D] SDF format, chain SB [auth D] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain UA [auth C] SDF format, chain UB [auth D] SDF format, chain VA [auth C] SDF format, chain VB [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C]	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		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain VA [auth C] Focus chain VB [auth D] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain I [auth A] SDF format, chain MB [auth D] SDF format, chain SA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain SA [auth C]	CA [auth B], I [auth A], MB [auth D], SA [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain CA [auth B] Focus chain I [auth A] Focus chain MB [auth D] Focus chain SA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain I [auth A] Focus chain MB [auth D] Focus chain SA [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain MA [auth B] SDF format, chain S [auth A] SDF format, chain WB [auth D] MOL2 format, chain CB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain WB [auth D]	CB [auth C], MA [auth B], S [auth A], WB [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CB [auth C] Focus chain MA [auth B] Focus chain S [auth A] Focus chain WB [auth D] Interactions & Density Focus chain CB [auth C] Focus chain MA [auth B] Focus chain S [auth A] Focus chain WB [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	T [auth A], U [auth A], V [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Funding Organization	Location	Grant Number
The Rockefeller University	United 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