9EV8 | pdb_00009ev8

Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM calcium

PDB DOI: https://doi.org/10.2210/pdb9EV8/pdb
EM Map EMD-19994: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Desulfofustis sp. PB-SRB1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-28 Released: 2025-04-09
Deposition Author(s): Fan, C., Howard, R.J., Lindahl, E.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel

Fan, C., Howard, R.J., Lindahl, E.

To be published.

Macromolecule Content

Total Structure Weight: 366.86 kDa
Atom Count: 23,390
Modelled Residue Count: 2,880
Deposited Residue Count: 3,210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neur_chan_LBD domain-containing protein	A, B, C, D, E	642	Desulfofustis sp. PB-SRB1	Mutation(s): 0 Gene Names: N839_03575
UniProt
Find proteins for V4JF97 (Desulfofustis sp. PB-SRB1) Explore V4JF97 Go to UniProtKB: V4JF97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V4JF97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX6 Query on PX6 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain N [auth A] SDF format, chain XA [auth E] SDF format, chain LA [auth D] SDF format, chain QA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain LA [auth D] MOL2 format, chain QA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain XA [auth E] mmCIF format, chain LA [auth D] mmCIF format, chain QA [auth E]	CA [auth C], LA [auth D], N [auth A], QA [auth E], XA [auth E]	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE C₃₅ H₆₈ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-M		Interactions Focus chain CA [auth C] Focus chain LA [auth D] Focus chain N [auth A] Focus chain QA [auth E] Focus chain XA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain LA [auth D] Focus chain N [auth A] Focus chain QA [auth E] Focus chain XA [auth E]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain T [auth B] SDF format, chain WA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain WA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain WA [auth E]	BA [auth C], K [auth A], KA [auth D], T [auth B], WA [auth E]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain T [auth B] Focus chain WA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain T [auth B] Focus chain WA [auth E]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain TA [auth E] SDF format, chain Y [auth C] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain Q [auth B] SDF format, chain UA [auth E] SDF format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain Z [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain Y [auth C] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain Z [auth C]	H [auth A] HA [auth D] I [auth A] IA [auth D] Q [auth B] H [auth A], HA [auth D], I [auth A], IA [auth D], Q [auth B], R [auth B], TA [auth E], UA [auth E], Y [auth C], Z [auth C]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain Y [auth C] Focus chain Z [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain S [auth B] SDF format, chain VA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain VA [auth E]	AA [auth C], J [auth A], JA [auth D], S [auth B], VA [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain S [auth B] Focus chain VA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain S [auth B] Focus chain VA [auth E]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain SA [auth E] SDF format, chain V [auth B] SDF format, chain X [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain X [auth C]	EA [auth C] G [auth A] GA [auth D] M [auth A] NA [auth D] EA [auth C], G [auth A], GA [auth D], M [auth A], NA [auth D], P [auth B], PA [auth E], SA [auth E], V [auth B], X [auth C]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain M [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain PA [auth E] Focus chain SA [auth E] Focus chain V [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain M [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain PA [auth E] Focus chain SA [auth E] Focus chain V [auth B] Focus chain X [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain MA [auth D] SDF format, chain O [auth B] SDF format, chain RA [auth E] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain L [auth A] SDF format, chain OA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth E]	DA [auth C] F [auth A] FA [auth D] L [auth A] MA [auth D] DA [auth C], F [auth A], FA [auth D], L [auth A], MA [auth D], O [auth B], OA [auth E], RA [auth E], U [auth B], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain L [auth A] Focus chain MA [auth D] Focus chain O [auth B] Focus chain OA [auth E] Focus chain RA [auth E] Focus chain U [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain L [auth A] Focus chain MA [auth D] Focus chain O [auth B] Focus chain OA [auth E] Focus chain RA [auth E] Focus chain U [auth B] Focus chain W [auth C]