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- PDB-5szk: Structure of human N-terminally engineered Rab1b in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5szk
TitleStructure of human N-terminally engineered Rab1b in complex with the bMERB domain of Mical-cL
Components
  • MICAL C-terminal-like protein
  • Ras-related protein Rab-1B
KeywordsENDOCYTOSIS / Mical-cL / DUF3585 / Mical / Rab effector / Rab1b / protein transport
Function / homology
Function and homology information


F-actin monooxygenase / positive regulation of glycoprotein metabolic process / sulfur oxidation / NAD(P)H oxidase H2O2-forming activity / 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 / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization ...F-actin monooxygenase / positive regulation of glycoprotein metabolic process / sulfur oxidation / NAD(P)H oxidase H2O2-forming activity / 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 / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / actin filament depolymerization / Golgi Cisternae Pericentriolar Stack Reorganization / mitogen-activated protein kinase binding / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / heart looping / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / cytoskeleton organization / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / FAD binding / small monomeric GTPase / G protein activity / actin filament / monooxygenase activity / intracellular protein transport / actin binding / heart development / oxidoreductase activity / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ProQ/FinO domain / ProQ/FINO family / 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 ...ProQ/FinO domain / ProQ/FINO family / 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 / [F-actin]-monooxygenase MICAL2 / Ras-related protein Rab-1B
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. / Gazdag, E.M. / Mueller, M.P.
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: 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: MICAL C-terminal-like protein
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3694
Polymers40,8222
Non-polymers5472
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-20 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.230, 117.030, 139.430
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 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
#2: Protein Ras-related protein Rab-1B


Mass: 22352.361 Da / Num. of mol.: 1 / Mutation: N2A, P3K, E4T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0U4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Mutation: N2A, P3K, E4T
Source method: isolated from a genetically manipulated source
Formula: Mg / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Mutation: N2A, P3K, E4T
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bis-tris pH 7.5, 0.2M sodium malonate and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91908 Å / Relative weight: 1
ReflectionResolution: 2.8→44.8 Å / Num. obs: 12904 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.079 / Net I/σ(I): 22.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.45 / CC1/2: 0.757 / % 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: 3NKV, 5SZG

3nkv

5szg


Resolution: 2.8→44.8 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.44
RfactorNum. reflection% reflection
Rfree0.2607 646 5.01 %
Rwork0.2075 --
obs0.2102 12904 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 3 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012626
X-RAY DIFFRACTIONf_angle_d1.1783527
X-RAY DIFFRACTIONf_dihedral_angle_d18.2091630
X-RAY DIFFRACTIONf_chiral_restr0.061395
X-RAY DIFFRACTIONf_plane_restr0.005447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01630.38381270.30752406X-RAY DIFFRACTION100
3.0163-3.31980.32781280.25812425X-RAY DIFFRACTION100
3.3198-3.79990.3241270.21982410X-RAY DIFFRACTION100
3.7999-4.78660.22541290.18972467X-RAY DIFFRACTION100
4.7866-44.82540.23041350.18832550X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.72131.41471.02015.2630.73623.9862-0.35830.4679-0.2449-0.72880.7941-0.33940.09770.44450.66080.5377-0.18040.1160.5346-0.13950.471422.517714.526-15.0487
21.19770.6994-0.41932.34850.3170.8884-0.39180.0690.0989-0.27620.1769-0.0662-0.1985-0.0848-0.00320.4257-0.0722-0.12370.51770.10260.511528.047540.8991-10.375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 1:173)
2X-RAY DIFFRACTION2(chain A and resseq 531:681)

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