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- PDB-5lpn: Structure of human Rab10 in complex with the bMERB domain of Mical-1 -

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Basic information

Entry
Database: PDB / ID: 5lpn
TitleStructure of human Rab10 in complex with the bMERB domain of Mical-1
Components
  • Protein-methionine sulfoxide oxidase MICAL1
  • Ras-related protein Rab-10
KeywordsENDOCYTOSIS / Mical-1 / DUF3585 / Mical / Rab effector / Rab10 / oxidoreductase
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum membrane / endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of neuroblast polarity / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / endoplasmic reticulum tubular network ...establishment of protein localization to endoplasmic reticulum membrane / endoplasmic reticulum tubular network organization / protein localization to basolateral plasma membrane / establishment of neuroblast polarity / hippocampal mossy fiber expansion / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / endoplasmic reticulum tubular network / regulation of regulated secretory pathway / insulin-responsive compartment / regulated exocytosis / NAD(P)H oxidase H2O2-forming activity / polarized epithelial cell differentiation / 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 / exocytic vesicle / Golgi to plasma membrane protein transport / cadherin binding involved in cell-cell adhesion / Golgi to plasma membrane transport / RAB geranylgeranylation / myosin V binding / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization / establishment of protein localization to membrane / endosomal transport / intermediate filament / intercellular bridge / actin filament bundle assembly / antigen processing and presentation / vesicle-mediated transport / cytoskeleton organization / FAD binding / axonogenesis / small monomeric GTPase / secretory granule membrane / G protein activity / negative regulation of protein phosphorylation / monooxygenase activity / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / trans-Golgi network / cytoplasmic vesicle membrane / cilium / recycling endosome / small GTPase binding / SH3 domain binding / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / actin filament binding / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / cytoskeleton / endosome membrane / endosome / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / 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 ...DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / 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 Rab1 family 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.8 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 FoundationSFB642, 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: PDBE / 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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-10
B: Protein-methionine sulfoxide oxidase MICAL1
C: Ras-related protein Rab-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3507
Polymers58,2573
Non-polymers1,0934
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-43 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 59.000, 198.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-10


Mass: 20202.314 Da / Num. of mol.: 2
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 Protein-methionine sulfoxide oxidase 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: 17852.303 Da / Num. of mol.: 1 / Fragment: UNP residues 918-1067
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, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6%-10% PEG8000 0.1M Imidazole / PH range: 7.6-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.8→44.004 Å / Num. obs: 17508 / % possible obs: 99.63 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.118 / Rsym value: 0.123 / Net I/σ(I): 14.12
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 3.25 / CC1/2: 0.803 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lhw and 5szg

4lhw

5szg


Resolution: 2.8→44.004 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.75
RfactorNum. reflection% reflection
Rfree0.2866 875 5 %
Rwork0.244 --
obs0.2462 17499 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 66 4 3747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083793
X-RAY DIFFRACTIONf_angle_d1.1185125
X-RAY DIFFRACTIONf_dihedral_angle_d20.5152282
X-RAY DIFFRACTIONf_chiral_restr0.06589
X-RAY DIFFRACTIONf_plane_restr0.006644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97550.36621430.30522705X-RAY DIFFRACTION99
2.9755-3.20510.37291430.29272713X-RAY DIFFRACTION99
3.2051-3.52760.32811410.26922709X-RAY DIFFRACTION99
3.5276-4.03770.27621450.25082757X-RAY DIFFRACTION100
4.0377-5.08590.27471470.21532792X-RAY DIFFRACTION100
5.0859-44.00980.25461560.23062948X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.7086 Å / Origin y: 73.9068 Å / Origin z: 216.9504 Å
111213212223313233
T0.339 Å20.0622 Å2-0.0207 Å2-0.3542 Å2-0.0427 Å2--0.3078 Å2
L0.7826 °2-0.5522 °20.2051 °2-0.7247 °2-0.6177 °2--1.0177 °2
S-0.0376 Å °-0.2198 Å °-0.1146 Å °0.2532 Å °0.1731 Å °-0.0524 Å °-0.2518 Å °-0.1436 Å °0.0247 Å °
Refinement TLS groupSelection details: all

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