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- PDB-3bc1: Crystal Structure of the complex Rab27a-Slp2a -

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Basic information

Entry
Database: PDB / ID: 3bc1
TitleCrystal Structure of the complex Rab27a-Slp2a
Components
  • Ras-related protein Rab-27A
  • Synaptotagmin-like protein 2
KeywordsSIGNALING PROTEIN/TRANSPORT PROTEIN / Rab27 / GTPase / Rab / signaling protein / GDPNP / Slp2a / Exophilin-4 / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / SIGNALING PROTEIN-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


multivesicular body organization / cytotoxic T cell degranulation / pigment granule localization / positive regulation of constitutive secretory pathway / pigment granule transport / positive regulation of regulated secretory pathway / melanosome localization / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / natural killer cell degranulation ...multivesicular body organization / cytotoxic T cell degranulation / pigment granule localization / positive regulation of constitutive secretory pathway / pigment granule transport / positive regulation of regulated secretory pathway / melanosome localization / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / natural killer cell degranulation / exosomal secretion / Weibel-Palade body / melanosome transport / neurexin family protein binding / exocytic vesicle / melanocyte differentiation / multivesicular body sorting pathway / myosin V binding / vesicle docking involved in exocytosis / multivesicular body membrane / complement-dependent cytotoxicity / pigmentation / positive regulation of reactive oxygen species biosynthetic process / phosphatidylserine binding / exocytosis / positive regulation of exocytosis / antigen processing and presentation / photoreceptor outer segment / protein targeting / phosphatase binding / positive regulation of phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / small monomeric GTPase / secretory granule membrane / secretory granule / intracellular protein transport / small GTPase binding / GDP binding / blood coagulation / melanosome / late endosome / lysosome / apical plasma membrane / protein domain specific binding / GTPase activity / dendrite / positive regulation of gene expression / GTP binding / Golgi apparatus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3000 / Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3000 / Synaptotagmin-like 1-5, C2B domain / Rab27a/b / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / C2 domain superfamily / Small GTPase / Ras family / Helix non-globular / Special / 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-27A / Synaptotagmin-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChavas, L.M.G. / Ihara, K. / Kawasaki, M. / Wakatsuki, S.
CitationJournal: Structure / Year: 2008
Title: Elucidation of Rab27 recruitment by its effectors: structure of Rab27a bound to Exophilin4/Slp2-a
Authors: Chavas, L.M.G. / Ihara, K. / Kawasaki, M. / Torii, S. / Uejima, T. / Kato, R. / Izumi, T. / Wakatsuki, S.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE The sequence database for chain B, F is Q9HCH5-3, isoform 3.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-27A
B: Synaptotagmin-like protein 2
E: Ras-related protein Rab-27A
F: Synaptotagmin-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5418
Polymers58,4484
Non-polymers1,0934
Water6,323351
1
A: Ras-related protein Rab-27A
B: Synaptotagmin-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7704
Polymers29,2242
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-28 kcal/mol
Surface area12660 Å2
MethodPISA
2
E: Ras-related protein Rab-27A
F: Synaptotagmin-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7704
Polymers29,2242
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-27 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.505, 77.777, 115.011
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-27A


Mass: 22214.016 Da / Num. of mol.: 2 / Fragment: residues in database 1-193 / Mutation: C123S C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LysS / References: UniProt: Q9ERI2, small monomeric GTPase
#2: Protein Synaptotagmin-like protein 2 / Slp2-a / Exophilin-4


Mass: 7009.934 Da / Num. of mol.: 2 / Fragment: Slp2a Rab-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LysS / References: UniProt: Q9HCH5
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na Citrate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.345 Å / Num. obs: 45347 / % possible obs: 95.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.25 / Num. unique all: 4408 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IF0

2if0


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.422 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24474 2209 5.1 %RANDOM
Rwork0.19914 ---
obs0.20145 41151 95.77 %-
all-45347 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 66 351 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223909
X-RAY DIFFRACTIONr_bond_other_d0.0010.022708
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9755267
X-RAY DIFFRACTIONr_angle_other_deg0.82536542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2975458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23324.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24615707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.741533
X-RAY DIFFRACTIONr_chiral_restr0.0580.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
X-RAY DIFFRACTIONr_nbd_refined0.2040.2768
X-RAY DIFFRACTIONr_nbd_other0.1820.22835
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21853
X-RAY DIFFRACTIONr_nbtor_other0.0810.22010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6761.53004
X-RAY DIFFRACTIONr_mcbond_other0.1041.5944
X-RAY DIFFRACTIONr_mcangle_it0.7523655
X-RAY DIFFRACTIONr_scbond_it1.19931920
X-RAY DIFFRACTIONr_scangle_it1.784.51612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 148 -
Rwork0.264 3102 -
obs--97.86 %
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)
10.2065-0.03430.02160.3052-0.05150.7210.0081-0.05340.0580.0292-0.02970.0023-0.07330.03160.0216-0.0185-0.0079-0.0021-0.0668-0.0013-0.040916.497116.4512-28.5018
22.80561.1307-0.31481.42860.11670.5017-0.0516-0.1311-0.053-0.04710.0064-0.13640.00920.12370.0452-0.01980.0226-0.0302-0.02660.0439-0.083930.62353.4443-23.0899
30.6373-0.0877-0.17780.7540.07980.58510.00460.0394-0.0190.0271-0.0075-0.0391-0.02090.07310.0028-0.07910.0064-0.0081-0.07450.0022-0.084427.6313-7.2757-1.182
42.49870.71210.33310.76940.23080.71630.00840.0513-0.0536-0.0374-0.0065-0.0594-0.06940.0581-0.0019-0.01210.00220.0015-0.0689-0.0081-0.012727.095112.6523-5.2129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 188
2X-RAY DIFFRACTION2B5 - 56
3X-RAY DIFFRACTION3E4 - 55
4X-RAY DIFFRACTION3E65 - 187
5X-RAY DIFFRACTION4F5 - 55

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