9LN9 | pdb_00009ln9

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

PDB DOI: https://doi.org/10.2210/pdb9LN9/pdb
EM Map EMD-63229: EMDB EMDataResource

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

Deposited: 2025-01-21 Released: 2026-01-28
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: 2.97 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

Sixteen polymer 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: 598.52 kDa
Atom Count: 37,626
Modeled Residue Count: 4,708
Deposited Residue Count: 5,309
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer mitochondrial transmembrane helix translocase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	330	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
An unknown peptide substrate	Q	29	Escherichia coli BL21(DE3)	Mutation(s): 0
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 Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain RA [auth N] SDF format, chain R [auth A] SDF format, chain PA [auth M] SDF format, chain NA [auth L] SDF format, chain LA [auth K] SDF format, chain JA [auth J] SDF format, chain HA [auth I] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth N] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth M] MOL2 format, chain NA [auth L] MOL2 format, chain LA [auth K] MOL2 format, chain JA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth N] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth M] mmCIF format, chain NA [auth L] mmCIF format, chain LA [auth K] mmCIF format, chain JA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] DA [auth G] FA [auth H] HA [auth I] JA [auth J] BA [auth F], DA [auth G], FA [auth H], HA [auth I], JA [auth J], LA [auth K], NA [auth L], PA [auth M], R [auth A], RA [auth N], T [auth B], V [auth C], X [auth D], Z [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain JA [auth J] Focus chain LA [auth K] Focus chain NA [auth L] Focus chain PA [auth M] Focus chain R [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain U [auth B] SDF format, chain SA [auth N] SDF format, chain S [auth A] SDF format, chain QA [auth M] SDF format, chain OA [auth L] SDF format, chain MA [auth K] SDF format, chain KA [auth J] SDF format, chain IA [auth I] SDF format, chain GA [auth H] SDF format, chain EA [auth G] SDF format, chain CA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth N] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth M] MOL2 format, chain OA [auth L] MOL2 format, chain MA [auth K] MOL2 format, chain KA [auth J] MOL2 format, chain IA [auth I] MOL2 format, chain GA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth N] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth M] mmCIF format, chain OA [auth L] mmCIF format, chain MA [auth K] mmCIF format, chain KA [auth J] mmCIF format, chain IA [auth I] mmCIF format, chain GA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth F] EA [auth G] GA [auth H] IA [auth I] AA [auth E], CA [auth F], EA [auth G], GA [auth H], IA [auth I], KA [auth J], MA [auth K], OA [auth L], QA [auth M], S [auth A], SA [auth N], U [auth B], W [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain S [auth A] Focus chain SA [auth N] Focus chain U [auth B] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain MA [auth K] Focus chain OA [auth L] Focus chain QA [auth M] Focus chain S [auth A] Focus chain SA [auth N] Focus chain U [auth B] Focus chain W [auth C] Focus chain Y [auth D]