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- PDB-6ixv: Crystal structure of SH3BP5-Rab11a -

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Basic information

Entry
Database: PDB / ID: 6ixv
TitleCrystal structure of SH3BP5-Rab11a
Components
  • Ras-related protein Rab-11A
  • SH3 domain-binding protein 5
KeywordsSIGNALING PROTEIN / Rab11 / GEF / SH3BP5
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / regulation of endocytic recycling / establishment of protein localization to organelle / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization / exosomal secretion / amyloid-beta clearance by transcytosis / regulation of cilium assembly / regulation of protein transport / presynaptic endosome / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein transmembrane transport / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / melanosome transport / multivesicular body assembly / protein localization to cilium / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / protein kinase inhibitor activity / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / phagocytic vesicle / vesicle-mediated transport / multivesicular body / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / SH3 domain binding / Schaffer collateral - CA1 synapse / recycling endosome membrane / neuron projection development / spindle pole / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / synaptic vesicle membrane / G protein activity / cytoplasmic vesicle / microtubule binding / vesicle / intracellular signal transduction / nuclear body / Golgi membrane / GTPase activity / centrosome / GTP binding / glutamatergic synapse / Golgi apparatus / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
SH3-binding 5 / SH3 domain-binding protein 5 (SH3BP5) / : / Small GTPase Rab 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 ...SH3-binding 5 / SH3 domain-binding protein 5 (SH3BP5) / : / Small GTPase Rab 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 / 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
PHOSPHATE ION / SH3 domain-binding protein 5 / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15072 Japan
CitationJournal: Life Sci Alliance / Year: 2019
Title: Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Authors: Goto-Ito, S. / Morooka, N. / Yamagata, A. / Sato, Y. / Sato, K. / Fukai, S.
History
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SH3 domain-binding protein 5
B: SH3 domain-binding protein 5
C: SH3 domain-binding protein 5
D: SH3 domain-binding protein 5
E: Ras-related protein Rab-11A
F: Ras-related protein Rab-11A
G: Ras-related protein Rab-11A
H: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,98611
Polymers203,7018
Non-polymers2853
Water00
1
A: SH3 domain-binding protein 5
E: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0203
Polymers50,9252
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-17 kcal/mol
Surface area24710 Å2
MethodPISA
2
B: SH3 domain-binding protein 5
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0203
Polymers50,9252
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area25290 Å2
MethodPISA
3
C: SH3 domain-binding protein 5
G: Ras-related protein Rab-11A


Theoretical massNumber of molelcules
Total (without water)50,9252
Polymers50,9252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-13 kcal/mol
Surface area24530 Å2
MethodPISA
4
D: SH3 domain-binding protein 5
H: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0203
Polymers50,9252
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-20 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.806, 199.075, 303.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
SH3 domain-binding protein 5 / SH3BP-5 / SH3 domain-binding protein that preferentially associates with BTK


Mass: 31184.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3BP5, SAB / Production host: Escherichia coli (E. coli) / References: UniProt: O60239
#2: Protein
Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 19741.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

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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: 4.37 Å3/Da / Density % sol: 71.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6M NaCl, 0.1M NaH2PO4 pH 6.8, 16% PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 35583 / % possible obs: 100 % / Redundancy: 32.6 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 41.1
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 1.546 / Num. unique obs: 1505

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.769 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1753 4.93 %
Rwork0.2286 --
obs0.23 35564 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→49.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12735 0 15 0 12750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112909
X-RAY DIFFRACTIONf_angle_d0.46117339
X-RAY DIFFRACTIONf_dihedral_angle_d8.6664989
X-RAY DIFFRACTIONf_chiral_restr0.0161933
X-RAY DIFFRACTIONf_plane_restr0.0022241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8004-3.90310.36771580.31852526X-RAY DIFFRACTION99
3.9031-4.01790.36641200.31052556X-RAY DIFFRACTION100
4.0179-4.14760.35191400.30372583X-RAY DIFFRACTION100
4.1476-4.29570.35611430.28942549X-RAY DIFFRACTION100
4.2957-4.46760.30321420.27722568X-RAY DIFFRACTION100
4.4676-4.67080.31831310.25072590X-RAY DIFFRACTION100
4.6708-4.91690.28931380.24242586X-RAY DIFFRACTION100
4.9169-5.22460.30541350.25272572X-RAY DIFFRACTION100
5.2246-5.62750.38021350.30782621X-RAY DIFFRACTION100
5.6275-6.19290.34411230.30392625X-RAY DIFFRACTION100
6.1929-7.08680.30861260.262621X-RAY DIFFRACTION100
7.0868-8.92020.22451170.19332662X-RAY DIFFRACTION100
8.9202-49.7730.18771450.18442752X-RAY DIFFRACTION99

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