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- PDB-5szi: Structure of human Rab8a in complex with the bMERB domain of Mical-cL -

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Basic information

Entry
Database: PDB / ID: 5szi
TitleStructure of human Rab8a in complex with the bMERB domain of Mical-cL
Components
  • MICAL C-terminal-like protein
  • Ras-related protein Rab-8A
KeywordsENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab8a / transport protein
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / Golgi vesicle fusion to target membrane / regulation of protein transport / NAD(P)H oxidase H2O2-forming activity / neurotransmitter receptor transport, endosome to postsynaptic membrane / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium ...neurotransmitter receptor transport to postsynaptic membrane / F-actin monooxygenase / F-actin monooxygenase activity / sulfur oxidation / Golgi vesicle fusion to target membrane / regulation of protein transport / NAD(P)H oxidase H2O2-forming activity / neurotransmitter receptor transport, endosome to postsynaptic membrane / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / 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 / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / TBC/RABGAPs / mitogen-activated protein kinase binding / vesicle docking involved in exocytosis / ciliary membrane / heart looping / ciliary base / Golgi organization / exocytosis / cilium assembly / phagocytic vesicle / cytoskeleton organization / FAD binding / centriole / Anchoring of the basal body to the plasma membrane / axonogenesis / protein tyrosine kinase binding / trans-Golgi network membrane / small monomeric GTPase / protein localization to plasma membrane / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / monooxygenase activity / regulation of long-term neuronal synaptic plasticity / autophagy / small GTPase binding / centriolar satellite / phagocytic vesicle membrane / cellular response to insulin stimulus / recycling endosome membrane / synaptic vesicle / GDP binding / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / heart development / actin binding / midbody / oxidoreductase activity / lysosome / endosome / endosome membrane / regulation of autophagy / cilium / ciliary basal body / Golgi membrane / neuronal cell body / GTPase activity / dendrite / centrosome / GTP binding / nucleolus / glutamatergic synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / metal ion binding / nucleus / 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 / Ras-related protein Rab-8A / [F-actin]-monooxygenase MICAL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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

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Assembly

Deposited unit
A: Ras-related protein Rab-8A
B: MICAL C-terminal-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9144
Polymers42,3672
Non-polymers5472
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.400, 122.400, 139.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ras-related protein Rab-8A / Oncogene c-mel


Mass: 23897.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006
#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
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M bis tris propane 0.2M tri sodium citrate 20% PEG 3350
PH range: 8.3-8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00009 Å / Relative weight: 1
ReflectionResolution: 2.85→46 Å / Num. obs: 12810 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.092 / Net I/σ(I): 16.45
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.507 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10-2155_1692: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHW, 5SZG

4lhw

5szg


Resolution: 2.85→45.952 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.2884 641 5 %
Rwork0.237 --
obs0.2396 12808 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→45.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 0 2 2461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092487
X-RAY DIFFRACTIONf_angle_d1.1753361
X-RAY DIFFRACTIONf_dihedral_angle_d20.3361508
X-RAY DIFFRACTIONf_chiral_restr0.061385
X-RAY DIFFRACTIONf_plane_restr0.005433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8502-3.07020.351250.31112380X-RAY DIFFRACTION100
3.0702-3.37910.27921270.27692404X-RAY DIFFRACTION100
3.3791-3.86780.28361270.24482409X-RAY DIFFRACTION100
3.8678-4.87220.2931280.22132439X-RAY DIFFRACTION100
4.8722-45.95810.28171340.22622535X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.4498 Å / Origin y: 45.9171 Å / Origin z: -14.3057 Å
111213212223313233
T0.4312 Å2-0.1764 Å2-0.1318 Å2-0.4485 Å2-0.0427 Å2--0.3783 Å2
L1.707 °20.337 °2-1.2669 °2-4.9765 °2-3.7608 °2--3.293 °2
S-0.5241 Å °0.3991 Å °-0.0477 Å °-0.1895 Å °0.7919 Å °-0.2356 Å °-0.0978 Å °-0.347 Å °0.7031 Å °
Refinement TLS groupSelection details: (chain A and resseq 2:400)

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