9L3U | pdb_00009l3u

Heptamer Msp1 from S.cerevisiae(with a catalytic dead mutation) in complex with an unknown peptide substrate

PDB DOI: https://doi.org/10.2210/pdb9L3U/pdb
EM Map EMD-62789: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-19 Released: 2025-12-24
Deposition Author(s): Chengdong, H., Simin, W., Xuan, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 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

Heptamer Msp1 from S.cerevisiae(with a catalytic dead mutation) in complex with an unknown peptide substrate

Chengdong, H., Simin, W., Xuan, C.

To be published.

Macromolecule Content

Total Structure Weight: 287.75 kDa
Atom Count: 16,352
Modeled Residue Count: 2,044
Deposited Residue Count: 2,549
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
An unknown peptide substrate	A [auth H]	15	Saccharomyces cerevisiae S288C	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer mitochondrial transmembrane helix translocase	B [auth A] C [auth B] D [auth C] E [auth D] F [auth E] B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G]	362	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: MSP1, YTA4, YGR028W EC: 7.4.2
UniProt
Find proteins for P28737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P28737 Go to UniProtKB: P28737
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28737
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G]	I [auth A] K [auth B] N [auth C] P [auth D] Q [auth E] I [auth A], K [auth B], N [auth C], P [auth D], Q [auth E], S [auth F], U [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain R [auth E] SDF format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain R [auth E] MOL2 format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain R [auth E] mmCIF format, chain J [auth A]	J [auth A] L [auth B] M [auth B] O [auth C] R [auth E] J [auth A], L [auth B], M [auth B], O [auth C], R [auth E], T [auth F], V [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G]