9E2P | pdb_00009e2p

Complex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613)

PDB DOI: https://doi.org/10.2210/pdb9E2P/pdb
EM Map EMD-47460: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-22 Released: 2025-07-09
Deposition Author(s): Ravitch, E.E., Baltrusaitis, E.E., Barrie, K.R., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.57 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9E2P

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

Literature

Complex of Human MIRO1 and TRAK1 Binding Site-2 (L570-R613)

Ravitch, E.E., Baltrusaitis, E.E., Perez, T.P., Barrie, K.R., Fenton, A.R., Holbaur, E.L.F., Dominguez, R.

To be published.

Macromolecule Content

Total Structure Weight: 157.59 kDa
Atom Count: 10,282
Modeled Residue Count: 1,262
Deposited Residue Count: 1,354
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial Rho GTPase 1	A, C	618	Homo sapiens	Mutation(s): 0 Gene Names: RHOT1, ARHT1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXI2 (Homo sapiens) Explore Q8IXI2 Go to UniProtKB: Q8IXI2
PHAROS: Q8IXI2 GTEx: ENSG00000126858
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IXI2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trafficking kinesin protein 1	B, D	59	Homo sapiens	Mutation(s): 0 Gene Names: TRAK1
UniProt
Find proteins for A0A8C9AJS8 (Prolemur simus) Explore A0A8C9AJS8 Go to UniProtKB: A0A8C9AJS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8C9AJS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth C]	E [auth A], G [auth A], J [auth C], L [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	H [auth A], I [auth A], M [auth C], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth C] Focus chain N [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.57 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Baltrusaitis, E.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RM1 GM136511

Revision History (Full details and data files)

Version 1.0: 2025-07-09
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.