9G0D | pdb_00009g0d

Structure of human Mical1 bMERB_V978A domain:Rab10 complex.

• PDB DOI: https://doi.org/10.2210/pdb9G0D/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-08 Released: 2025-07-02 
• Deposition Author(s): Rai, A., Goody, R.S.
• Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Biochemical and structural insights into the auto-inhibited state of Mical1 and its activation by Rab8

Rai, A., Janning, P., Vetter, I.R., Goody, R.S.

(2024) Elife 

• DOI: https://doi.org/10.7554/elife.102375.1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 38.57 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 316 
• Deposited Residue Count: 330 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[F-actin]-monooxygenase MICAL1	A [auth B]	153	Homo sapiens	Mutation(s): 1  Gene Names: MICAL1, MICAL, NICAL EC: 1.14.13.225 (PDB Primary Data), 1.6.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDZ2 (Homo sapiens) Explore Q8TDZ2  Go to UniProtKB:  Q8TDZ2
PHAROS:  Q8TDZ2 GTEx:  ENSG00000135596

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-10	B [auth C]	177	Homo sapiens	Mutation(s): 0  Gene Names: RAB10 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61026 (Homo sapiens) Explore P61026  Go to UniProtKB:  P61026
PHAROS:  P61026 GTEx:  ENSG00000084733

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	C	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.77	α = 90
b = 49.65	β = 98.54
c = 79.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Rai, A., Goody, R.S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	grant GO 284/10-1

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release