9LWN | pdb_00009lwn

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

PDB DOI: https://doi.org/10.2210/pdb9LWN/pdb
EM Map EMD-63451: EMDB EMDataResource

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

Deposited: 2025-02-15 Released: 2026-03-04
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: 3.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9LWN

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

Literature

Nonamer 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: 337.76 kDa
Atom Count: 21,453
Modeled Residue Count: 2,689
Deposited Residue Count: 2,992
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer mitochondrial transmembrane helix translocase	A [auth C] B C [auth D] D [auth E] E [auth F] A [auth C], B, C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth A]	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: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
An unknown peptide substrate	J	22	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 Y [auth I] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth B] SDF format, chain K [auth C] SDF format, chain AA [auth A] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth B] MOL2 format, chain K [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth B] mmCIF format, chain K [auth C] mmCIF format, chain AA [auth A]	AA [auth A] K [auth C] M [auth B] O [auth D] Q [auth E] AA [auth A], K [auth C], M [auth B], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H], Y [auth I]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth A] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I] Interactions & Density Focus chain AA [auth A] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth B] SDF format, chain L [auth C] SDF format, chain BA [auth A] MOL2 format, chain Z [auth I] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth B] MOL2 format, chain L [auth C] MOL2 format, chain BA [auth A] mmCIF format, chain Z [auth I] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth B] mmCIF format, chain L [auth C] mmCIF format, chain BA [auth A]	BA [auth A] L [auth C] N [auth B] P [auth D] R [auth E] BA [auth A], L [auth C], N [auth B], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H], Z [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I] Interactions & Density Focus chain BA [auth A] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-04

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: 2026-03-04
Type: Initial release

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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.