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- PDB-5low: Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 comple... -

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Basic information

Entry
Database: PDB / ID: 5low
TitleStructure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)
Components
  • (Synaptosomal-associated protein ...) x 2
  • Rabphilin-3A
KeywordsEXOCYTOSIS / membrane fusion / calcium / 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 / SNARE complex / SNAP receptor activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / positive regulation of hormone secretion / regulation of NMDA receptor activity / neurotransmitter secretion / dendritic spine organization / extrinsic component of membrane / syntaxin-1 binding / endosomal transport / Neutrophil degranulation / SNARE complex assembly / regulation of synapse assembly / myosin binding / synaptic vesicle priming / phosphate ion binding / regulation of neuron projection development / exocytosis / associative learning / synaptic vesicle exocytosis / voltage-gated potassium channel activity / long-term memory / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / somatodendritic compartment / voltage-gated potassium channel complex / photoreceptor inner segment / axonogenesis / secretory granule / SNARE binding / filopodium / locomotory behavior / neuromuscular junction / intracellular protein transport / trans-Golgi network / positive regulation of insulin secretion / phospholipid binding / small GTPase binding / long-term synaptic potentiation / neuron differentiation / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / lamellipodium / actin cytoskeleton / presynaptic membrane / growth cone / cell cortex / vesicle / dendritic spine / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / neuron projection / endosome / protein domain specific binding / axon / neuronal cell body / calcium ion binding / synapse / lipid 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: 2.8 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C.
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 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry

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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
H: Rabphilin-3A
I: Rabphilin-3A
J: Rabphilin-3A
K: Synaptosomal-associated protein 25
L: Synaptosomal-associated protein 25
M: Synaptosomal-associated protein 25
N: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,85933
Polymers191,73314
Non-polymers1,12619
Water1,69394
1
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)96,38316
Polymers95,8677
Non-polymers5179
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Rabphilin-3A
I: Rabphilin-3A
J: Rabphilin-3A
K: Synaptosomal-associated protein 25
L: Synaptosomal-associated protein 25
M: Synaptosomal-associated protein 25
N: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,47517
Polymers95,8677
Non-polymers60910
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.080, 239.496, 71.487
Angle α, β, γ (deg.)90.00, 114.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCHIJ

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


Mass: 18579.307 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rph3a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P47709

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Synaptosomal-associated protein ... , 2 types, 8 molecules DFKMEGLN

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


Mass: 10841.079 Da / Num. of mol.: 4
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: 9223.266 Da / Num. of mol.: 4
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, 113 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.537
11-H, -K, H+L20.463
ReflectionResolution: 2.8→47.9 Å / Num. obs: 43944 / % possible obs: 98.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 4.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.4 % / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOB

5lob


Resolution: 2.8→45.03 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.851 / SU B: 8.482 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26857 2212 5 %RANDOM
Rwork0.23793 ---
obs0.23944 41690 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.33 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å20 Å2-0.66 Å2
2--0.46 Å2-0 Å2
3----6.78 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11138 0 54 94 11286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210987
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.95715150
X-RAY DIFFRACTIONr_angle_other_deg0.798325352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2751362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1525.4600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.223152293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5361574
X-RAY DIFFRACTIONr_chiral_restr0.0560.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022537
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4984.6625486
X-RAY DIFFRACTIONr_mcbond_other0.4984.6625485
X-RAY DIFFRACTIONr_mcangle_it0.9036.9886835
X-RAY DIFFRACTIONr_mcangle_other0.9036.9886836
X-RAY DIFFRACTIONr_scbond_it0.2874.6875855
X-RAY DIFFRACTIONr_scbond_other0.2874.6875855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.547.028316
X-RAY DIFFRACTIONr_long_range_B_refined2.14635.03412133
X-RAY DIFFRACTIONr_long_range_B_other2.14635.03412133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.804→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 166 -
Rwork0.293 2927 -
obs--92.47 %

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