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- PDB-5szh: Structure of human Rab1b in complex with the bMERB domain of Mical-cL -

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Basic information

Entry
Database: PDB / ID: 5szh
TitleStructure of human 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


positive regulation of glycoprotein metabolic process / F-actin monooxygenase / F-actin monooxygenase activity / 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 / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / actin filament depolymerization ...positive regulation of glycoprotein metabolic process / F-actin monooxygenase / F-actin monooxygenase activity / 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 / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / mitogen-activated protein kinase binding / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / heart looping / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / cytoskeleton organization / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / FAD binding / small monomeric GTPase / actin filament / intracellular protein transport / monooxygenase activity / heart development / actin binding / G protein activity / cytoskeleton / oxidoreductase activity / Golgi membrane / GTPase activity / 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 / cytoplasm / cytosol
Similarity search - Function
: / ProQ/FinO domain / ProQ/FINO family / Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : ...: / 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 / [F-actin]-monooxygenase MICAL2 / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)41,4084
Polymers40,8612
Non-polymers5472
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.750, 129.380, 129.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

21B-413-

HOH

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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: 22391.330 Da / Num. of mol.: 1
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-22% PEG3350 0.1M bis-Tris Propane 0.2M tri-Sodium Citrate
PH range: 8.4-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→45.83 Å / Num. obs: 23533 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.105 / Rsym value: 0.109 / Net I/σ(I): 16.27
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.89 / CC1/2: 0.692 / % 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: 3NKV, 5SZG

3nkv

5szg


Resolution: 2.3→45.826 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2073 1176 5 %
Rwork0.1792 --
obs0.1807 23530 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 33 27 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082615
X-RAY DIFFRACTIONf_angle_d1.1043523
X-RAY DIFFRACTIONf_dihedral_angle_d15.683998
X-RAY DIFFRACTIONf_chiral_restr0.04396
X-RAY DIFFRACTIONf_plane_restr0.004451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40480.29791440.26942732X-RAY DIFFRACTION100
2.4048-2.53150.25991440.2492739X-RAY DIFFRACTION100
2.5315-2.69010.27711450.22382778X-RAY DIFFRACTION100
2.6901-2.89780.26681450.222755X-RAY DIFFRACTION100
2.8978-3.18930.26791470.21262778X-RAY DIFFRACTION100
3.1893-3.65070.24331470.18262792X-RAY DIFFRACTION100
3.6507-4.59880.15231490.14882843X-RAY DIFFRACTION100
4.5988-45.83470.17991550.16192928X-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)
12.2720.4150.79410.56380.39473.37230.0575-0.0391-0.1618-0.00430.011-0.03930.2484-0.1884-0.08080.44060.00020.01580.47990.03030.4519-30.0648-34.0777-47.8184
23.0898-1.008-0.31984.1920.67172.2212-0.00360.07350.1627-0.01960.0002-0.1066-0.06510.24540.00630.4279-0.0009-0.05020.41910.05280.4786-21.5022-11.1242-31.6661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 531:678)
2X-RAY DIFFRACTION2(chain B and resid 0:174)

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