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- PDB-2zet: Crystal structure of the small GTPase Rab27B complexed with the S... -

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Basic information

Entry
Database: PDB / ID: 2zet
TitleCrystal structure of the small GTPase Rab27B complexed with the Slp homology domain of Slac2-a/melanophilin
Components
  • Melanophilin
  • Ras-related protein Rab-27B
KeywordsSIGNALING PROTEIN / COMPLEX / GTP-BINDING PROTEIN / GTPASE / G-PROTEIN / RAB / RAB27B / EFFECTOR / MELANOPHILIN / Slp homology domain / Acetylation / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / Coiled coil / Metal-binding / Zinc / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


melanosome localization / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / unconventional myosin complex / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / melanocyte differentiation / Golgi stack ...melanosome localization / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / unconventional myosin complex / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / melanocyte differentiation / Golgi stack / multivesicular body sorting pathway / myosin V binding / regulation of exocytosis / trans-Golgi network transport vesicle / multivesicular body membrane / microtubule plus-end binding / pigmentation / microtubule organizing center / cortical actin cytoskeleton / myosin binding / exocytosis / positive regulation of exocytosis / synaptic vesicle endocytosis / protein targeting / stress fiber / axon cytoplasm / small monomeric GTPase / G protein activity / secretory granule / intracellular protein transport / synaptic vesicle membrane / small GTPase binding / GDP binding / melanosome / actin cytoskeleton / late endosome / actin binding / molecular adaptor activity / apical plasma membrane / protein domain specific binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding
Similarity search - Function
Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / Rab effector MyRIP/melanophilin C-terminus / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / small GTPase Rab1 family profile. / Zinc/RING finger domain, C3HC4 (zinc finger) ...Rab effector MyRIP/Melanophilin / Melanophilin, FYVE-related domain / Rab effector MyRIP/melanophilin C-terminus / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / small GTPase Rab1 family profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Zinc finger, FYVE/PHD-type / Small GTP-binding protein domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Melanophilin / Ras-related protein Rab-27B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKukimoto-Niino, M. / Sakamoto, A. / Kanno, E. / Hanawa-Suetsugu, K. / Terada, T. / Shirouzu, M. / Fukuda, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2008
Title: Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases.
Authors: Kukimoto-Niino, M. / Sakamoto, A. / Kanno, E. / Hanawa-Suetsugu, K. / Terada, T. / Shirouzu, M. / Fukuda, M. / Yokoyama, S.
History
DepositionDec 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-27B
C: Melanophilin
B: Ras-related protein Rab-27B
D: Melanophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,46414
Polymers81,9154
Non-polymers1,54910
Water1629
1
A: Ras-related protein Rab-27B
C: Melanophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7327
Polymers40,9572
Non-polymers7745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-53 kcal/mol
Surface area16380 Å2
MethodPISA
2
B: Ras-related protein Rab-27B
D: Melanophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7327
Polymers40,9572
Non-polymers7745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-53 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.208, 82.208, 325.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-27B


Mass: 23235.277 Da / Num. of mol.: 2 / Fragment: GTPase domain, UNP residues 1-201 / Mutation: Q78L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL FREE PROTEIN SYNTHESIS / Gene: Rab27b / Plasmid: PX070112-08 / References: UniProt: Q99P58
#2: Protein Melanophilin / / Exophilin-3 / Leaden protein / Synaptotagmin-like protein 2a / Slp homolog lacking C2 domains a / SlaC2-a


Mass: 17722.168 Da / Num. of mol.: 2 / Fragment: Slp homology domain, UNP residues 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL FREE PROTEIN SYNTHESIS / Gene: Slac2a / Plasmid: PX051201-06 / References: UniProt: Q91V27

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Non-polymers , 5 types, 19 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.65M (NH4)2SO4, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23600 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rsym value: 0.155 / Net I/σ(I): 16
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2.45 / Rsym value: 0.781 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→45.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2503339.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2311 9.9 %RANDOM
Rwork0.247 ---
obs0.247 23411 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.5647 Å2 / ksol: 0.305435 e/Å3
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.57 Å20 Å20 Å2
2--9.57 Å20 Å2
3----19.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 80 9 5297
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 326 8.6 %
Rwork0.367 3473 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gtp_paramgtp_Xplor_top

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