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- PDB-9g0d: Structure of human Mical1 bMERB_V978A domain:Rab10 complex. -

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Basic information

Entry
Database: PDB / ID: 9g0d
TitleStructure of human Mical1 bMERB_V978A domain:Rab10 complex.
Components
  • Ras-related protein Rab-10
  • [F-actin]-monooxygenase MICAL1
KeywordsENDOCYTOSIS / Mical / Rab GTPase / Complex / F-actin / Oxidation
Function / homology
Function and homology information


protein localization to basolateral plasma membrane / establishment of neuroblast polarity / endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / hippocampal mossy fiber expansion / secretory vesicle / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) ...protein localization to basolateral plasma membrane / establishment of neuroblast polarity / endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / hippocampal mossy fiber expansion / secretory vesicle / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / endoplasmic reticulum tubular network / regulation of regulated secretory pathway / regulated exocytosis / insulin-responsive compartment / NAD(P)H oxidase H2O2-forming activity / polarized epithelial cell differentiation / exocytic vesicle / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / cadherin binding involved in cell-cell adhesion / Golgi to plasma membrane transport / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / establishment of protein localization to membrane / intermediate filament / endosomal transport / antigen processing and presentation / exocytosis / actin filament bundle assembly / intercellular bridge / vesicle-mediated transport / cytoskeleton organization / FAD binding / axonogenesis / cytoplasmic vesicle membrane / secretory granule membrane / small monomeric GTPase / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adherens junction / actin filament / trans-Golgi network / monooxygenase activity / recycling endosome / small GTPase binding / SH3 domain binding / cellular response to insulin stimulus / phagocytic vesicle membrane / recycling endosome membrane / actin filament binding / GDP binding / actin cytoskeleton / actin binding / G protein activity / Factors involved in megakaryocyte development and platelet production / midbody / cytoskeleton / lysosome / endosome / endosome membrane / ciliary basal body / cilium / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-10 / [F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRai, A. / Goody, R.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)grant GO 284/10-1 Germany
CitationJournal: Elife / Year: 2024
Title: Biochemical and structural insights into the auto-inhibited state of Mical1 and its activation by Rab8
Authors: Rai, A. / Janning, P. / Vetter, I.R. / Goody, R.S.
History
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: [F-actin]-monooxygenase MICAL1
C: Ras-related protein Rab-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5734
Polymers38,0272
Non-polymers5472
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-23 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 49.650, 79.330
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein [F-actin]-monooxygenase MICAL1 / Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 17824.250 Da / Num. of mol.: 1 / Mutation: V978A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TDZ2, F-actin monooxygenase, NAD(P)H oxidase (H2O2-forming)
#2: Protein Ras-related protein Rab-10


Mass: 20202.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB10 / Production host: Escherichia coli (E. coli) / References: UniProt: P61026
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole pH 8.0, 5% (w/v) PEG 3000 and 30% (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.05→36.29 Å / Num. obs: 26092 / % possible obs: 99.3 % / Redundancy: 6.78 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.104 / Net I/σ(I): 11.36
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 1.338 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1923 / CC1/2: 0.799 / Rrim(I) all: 1.442 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.17.1-3660_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→36.29 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1304 5 %
Rwork0.2009 --
obs0.2032 26058 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 33 36 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072636
X-RAY DIFFRACTIONf_angle_d0.8083541
X-RAY DIFFRACTIONf_dihedral_angle_d6.469346
X-RAY DIFFRACTIONf_chiral_restr0.046395
X-RAY DIFFRACTIONf_plane_restr0.004452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.130.29571450.29732746X-RAY DIFFRACTION100
2.13-2.230.33211450.27252750X-RAY DIFFRACTION99
2.23-2.350.31491440.23612733X-RAY DIFFRACTION99
2.35-2.490.30041420.2372697X-RAY DIFFRACTION99
2.49-2.690.26581460.22992757X-RAY DIFFRACTION99
2.69-2.960.28241440.25012732X-RAY DIFFRACTION100
2.96-3.380.31041440.23242759X-RAY DIFFRACTION100
3.38-4.260.21431460.18452782X-RAY DIFFRACTION100
4.26-36.290.2051480.1542798X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 17.4721 Å / Origin y: 5.0196 Å / Origin z: 10.3005 Å
111213212223313233
T0.395 Å2-0.0219 Å2-0.0265 Å2-0.3391 Å20.0395 Å2--0.4038 Å2
L0.9833 °2-0.0152 °2-0.5448 °2-0.361 °2-0.345 °2--1.2955 °2
S0.0973 Å °-0.1401 Å °-0.1259 Å °-0.0424 Å °0.0009 Å °0.0445 Å °0.1336 Å °-0.2521 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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