8T56 | pdb_00008t56

Structure of mechanically activated ion channel OSCA1.2 in peptidiscs

PDB DOI: https://doi.org/10.2210/pdb8T56/pdb
EM Map EMD-41043: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Arabidopsis thaliana, synthetic construct
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2023-06-12 Released: 2023-12-27
Deposition Author(s): Burendei, B., Jojoa-Cruz, S., Lee, W.H., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain.

Jojoa-Cruz, S., Burendei, B., Lee, W.H., Ward, A.B.

(2024) Structure 32: 157

PubMed: 38103547 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2023.11.009
Primary Citation Related Structures:
8T56, 8T57

PubMed Abstract:
Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 225.4 kDa
Atom Count: 13,096
Modeled Residue Count: 1,498
Deposited Residue Count: 1,858
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium permeable stress-gated cation channel 1	A, B	781	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CSC1, At4g22120, F1N20.220 Membrane Entity: Yes
UniProt
Find proteins for Q5XEZ5 (Arabidopsis thaliana) Explore Q5XEZ5 Go to UniProtKB: Q5XEZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5XEZ5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NSPr peptide	C, D, E, F, G C, D, E, F, G, H, I, J	37	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain V [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain V [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain V [auth A]	HA [auth B], V [auth A]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain HA [auth B] Focus chain V [auth A] Interactions & Density Focus chain HA [auth B] Focus chain V [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B]	K [auth A], W [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain K [auth A] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain W [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JA [auth D] SDF format, chain MA [auth E] SDF format, chain OA [auth G] SDF format, chain PA [auth H] SDF format, chain SA [auth I] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain SA [auth I] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth H] mmCIF format, chain SA [auth I]	IA [auth C] JA [auth D] MA [auth E] OA [auth G] PA [auth H] IA [auth C], JA [auth D], MA [auth E], OA [auth G], PA [auth H], SA [auth I]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain IA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain OA [auth G] Focus chain PA [auth H] Focus chain SA [auth I] Interactions & Density Focus chain IA [auth C] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain OA [auth G] Focus chain PA [auth H] Focus chain SA [auth I]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth H] SDF format, chain R [auth A] SDF format, chain RA [auth H] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth I] SDF format, chain U [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth H] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth I] mmCIF format, chain U [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth A], NA [auth E], O [auth A], P [auth A], Q [auth A], QA [auth H], R [auth A], RA [auth H], S [auth A], T [auth A], TA [auth I], U [auth A], X [auth B], Y [auth B], Z [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth I] Focus chain U [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain RA [auth H] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth I] Focus chain U [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]