9EBA | pdb_00009eba

Human TRPML1 bound to Sybody57

PDB DOI: https://doi.org/10.2210/pdb9EBA/pdb
EM Map EMD-47875: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2024-11-12 Released: 2026-01-21
Deposition Author(s): Pumroy, R.P., Christensen, C.R., Salphati, S.P., Moiseenkova-Bell, V.Y., Newstead, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9EBA

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

Literature

Human TRPML1 bound to Sybody57

Salphati, S.P., Pumroy, R.P., Christensen, C.R., Moiseenkova-Bell, V.Y., Newstead, S.

To be published.

Macromolecule Content

Total Structure Weight: 330.37 kDa
Atom Count: 17,496
Modeled Residue Count: 2,188
Deposited Residue Count: 2,920
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sybody57	A [auth E], C [auth F], D [auth G], E [auth H]	150	synthetic construct	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucolipin-1	B [auth A], F [auth B], G [auth C], H [auth D]	580	Homo sapiens	Mutation(s): 0 Gene Names: MCOLN1, ML4, MSTP080
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZU1 (Homo sapiens) Explore Q9GZU1 Go to UniProtKB: Q9GZU1
PHAROS: Q9GZU1 GTEx: ENSG00000090674
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GZU1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EUJ (Subject of Investigation/LOI) Query on EUJ Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	I [auth A], J [auth B], K [auth C], L [auth D]	(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate C₂₅ H₄₉ O₁₉ P₃ QXHVLVSULWMTCV-DICZBTHZSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

Christensen, C.R.

Moiseenkova-Bell, V.Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144120

Revision History (Full details and data files)

Version 1.0: 2026-01-21
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.