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

Validation slider image for 9LN9

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28737
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
An unknown peptide substrate	Q	29	Escherichia coli BL21(DE3)	Mutation(s): 0

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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-01-28
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.