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- PDB-5szj: Structure of human Rab10 in complex with the bMERB domain of Mical-cL -

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Basic information

Entry
Database: PDB / ID: 5szj
TitleStructure of human Rab10 in complex with the bMERB domain of Mical-cL
Components
  • MICAL C-terminal-like protein
  • Ras-related protein Rab-10
KeywordsENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab10
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 / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / secretory vesicle / endoplasmic reticulum tubular network / insulin-responsive compartment ...protein localization to basolateral plasma membrane / establishment of neuroblast polarity / endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / secretory vesicle / endoplasmic reticulum tubular network / insulin-responsive compartment / polarized epithelial cell differentiation / NAD(P)H oxidase H2O2-forming activity / regulated exocytosis / 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 / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane transport / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / mitogen-activated protein kinase binding / endosomal transport / antigen processing and presentation / heart looping / exocytosis / vesicle-mediated transport / cytoskeleton organization / FAD binding / axonogenesis / secretory granule membrane / cytoplasmic vesicle membrane / small monomeric GTPase / protein localization to plasma membrane / adherens junction / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / monooxygenase activity / recycling endosome / phagocytic vesicle membrane / cellular response to insulin stimulus / recycling endosome membrane / GDP binding / heart development / actin binding / G protein activity / oxidoreductase activity / cytoskeleton / lysosome / endosome / endosome membrane / cilium / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ProQ/FinO domain / ProQ/FINO family / Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / LIM zinc-binding domain signature. ...ProQ/FinO domain / ProQ/FINO family / Mical, Rossman domain / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / DI(HYDROXYETHYL)ETHER / Ras-related protein Rab-10 / [F-actin]-monooxygenase MICAL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsRai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Mueller, M.P. / Gazdag, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 642, grant A4 Germany
Max Planck Society Germany
CitationJournal: Elife / Year: 2016
Title: bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Authors: Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Muller, M.P.
History
DepositionAug 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-10
B: MICAL C-terminal-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8915
Polymers41,2392
Non-polymers6533
Water70339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-16 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.680, 61.870, 55.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ras-related protein Rab-10


Mass: 22769.162 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
#2: Protein MICAL C-terminal-like protein / ERK2-binding testicular protein 1 / Ebitein-1


Mass: 18469.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICALCL / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZW33

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Non-polymers , 4 types, 42 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18%-22% PEG 3350 0.2-0.3 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→48.19 Å / Num. obs: 15861 / % possible obs: 99.96 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.137 / Rsym value: 0.143 / Net I/σ(I): 12.06
Reflection shellResolution: 2.66→2.7 Å / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.35 / CC1/2: 0.591 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHW, 5SZG

4lhw

5szg


Resolution: 2.66→48.19 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 793 5 %
Rwork0.2243 --
obs0.2264 15857 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 40 39 2638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042628
X-RAY DIFFRACTIONf_angle_d0.7563529
X-RAY DIFFRACTIONf_dihedral_angle_d16.0461006
X-RAY DIFFRACTIONf_chiral_restr0.025394
X-RAY DIFFRACTIONf_plane_restr0.002452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6601-2.82670.36931290.30232454X-RAY DIFFRACTION100
2.8267-3.0450.30011290.26462447X-RAY DIFFRACTION100
3.045-3.35130.29411310.24982488X-RAY DIFFRACTION100
3.3513-3.83610.27131300.22012486X-RAY DIFFRACTION100
3.8361-4.83240.24721340.1972531X-RAY DIFFRACTION100
4.8324-48.19820.24771400.21852658X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.8237 Å / Origin y: 23.8064 Å / Origin z: -30.851 Å
111213212223313233
T0.3788 Å2-0.0061 Å20.0469 Å2-0.3635 Å20.0695 Å2--0.4314 Å2
L1.0058 °2-0.2912 °20.136 °2-1.2385 °2-0.0138 °2--3.3267 °2
S0.0866 Å °0.0447 Å °0.0197 Å °0.0335 Å °0.0087 Å °0.1141 Å °0.0195 Å °-0.4969 Å °-0.0367 Å °
Refinement TLS groupSelection details: all

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