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- PDB-5lob: Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 s... -

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Basic information

Entry
Database: PDB / ID: 5lob
TitleStructure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)
Components
  • (Synaptosomal-associated protein ...) x 2
  • Rabphilin-3A
KeywordsEXOCYTOSIS / membrane fusion / SNARE complex / PIP2 / C2 domain
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex ...selenium binding / spontaneous neurotransmitter secretion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / cholinergic synapse / Dopamine Neurotransmitter Release Cycle / regulation of establishment of protein localization / positive regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / ribbon synapse / SNAP receptor activity / SNARE complex / inositol 1,4,5 trisphosphate binding / positive regulation of hormone secretion / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / neurotransmitter secretion / extrinsic component of membrane / syntaxin-1 binding / endosomal transport / Neutrophil degranulation / SNARE complex assembly / synaptic vesicle priming / regulation of synapse assembly / myosin binding / phosphate ion binding / regulation of neuron projection development / exocytosis / synaptic vesicle exocytosis / associative learning / voltage-gated potassium channel activity / long-term memory / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / photoreceptor inner segment / voltage-gated potassium channel complex / somatodendritic compartment / axonogenesis / secretory granule / SNARE binding / filopodium / intracellular protein transport / locomotory behavior / neuromuscular junction / trans-Golgi network / phospholipid binding / positive regulation of insulin secretion / small GTPase binding / long-term synaptic potentiation / neuron differentiation / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / actin cytoskeleton / lamellipodium / growth cone / presynaptic membrane / cell cortex / vesicle / dendritic spine / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / neuron projection / endosome / axon / protein domain specific binding / neuronal cell body / lipid binding / synapse / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / protein-containing complex / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. ...Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rabphilin-3A / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFerrer-Orta, C. / Verdaguer, N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural characterization of the Rabphilin-3A-SNAP25 interaction.
Authors: Ferrer-Orta, C. / Perez-Sanchez, M.D. / Coronado-Parra, T. / Silva, C. / Lopez-Martinez, D. / Baltanas-Copado, J. / Gomez-Fernandez, J.C. / Corbalan-Garcia, S. / Verdaguer, N.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rabphilin-3A
B: Rabphilin-3A
C: Rabphilin-3A
D: Synaptosomal-associated protein 25
E: Synaptosomal-associated protein 25
F: Synaptosomal-associated protein 25
G: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,13132
Polymers99,1017
Non-polymers2,03025
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-340 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.970, 58.754, 125.311
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Rabphilin-3A / Exophilin-1


Mass: 18579.307 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Details (production host): Kanamicine resistant / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P47709

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Synaptosomal-associated protein ... , 2 types, 4 molecules DFEG

#2: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 11266.603 Da / Num. of mol.: 2 / Fragment: N-terminal helix
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60881
#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 10414.731 Da / Num. of mol.: 2 / Fragment: C-terminal helix
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60881

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Non-polymers , 3 types, 25 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.9 Å3/Da / Density % sol: 54.7 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→48.42 Å / Num. obs: 12936 / % possible obs: 79.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 6
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
SCALAdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CM5

2cm5


Resolution: 3.3→42.527 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 632 4.89 %
Rwork0.24 --
obs0.2423 12926 77.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→42.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 110 0 5922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025972
X-RAY DIFFRACTIONf_angle_d0.3777967
X-RAY DIFFRACTIONf_dihedral_angle_d12.3943659
X-RAY DIFFRACTIONf_chiral_restr0.035828
X-RAY DIFFRACTIONf_plane_restr0.0021030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.55470.39111180.28352513X-RAY DIFFRACTION80
3.5547-3.91220.31221140.27182555X-RAY DIFFRACTION80
3.9122-4.47780.29771350.22322440X-RAY DIFFRACTION77
4.4778-5.63950.23151320.22722422X-RAY DIFFRACTION77
5.6395-42.5310.28031330.22872364X-RAY DIFFRACTION72
Refinement TLS params.Method: refined / Origin x: -49.1327 Å / Origin y: -17.4485 Å / Origin z: 1.3082 Å
111213212223313233
T0.4979 Å20.0584 Å20.0485 Å2-0.471 Å20.0186 Å2--0.4519 Å2
L0.6135 °2-0.0017 °20.2192 °2-0.0306 °20.016 °2--0.3459 °2
S0.046 Å °0.0209 Å °0.0341 Å °-0.0496 Å °-0.0453 Å °-0.0625 Å °0.0249 Å °-0.0039 Å °-0.0124 Å °
Refinement TLS groupSelection details: all

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