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- PDB-5lo8: The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 -

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Basic information

Entry
Database: PDB / ID: 5lo8
TitleThe C2B domain of Rabphilin 3A in complex with PI(4,5)P2
ComponentsRabphilin-3A
KeywordsPROTEIN TRANSPORT / vesicle fusion / PIP2 / C2 domain
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming ...selenium binding / spontaneous neurotransmitter secretion / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / synaptic vesicle priming / extrinsic component of membrane / exocytosis / phosphate ion binding / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / synaptic vesicle membrane / small GTPase binding / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PIO / Rabphilin-3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 8, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry / _struct_conn_type.id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55316
Polymers37,1592
Non-polymers2,39414
Water52229
1
A: Rabphilin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8709
Polymers18,5791
Non-polymers1,2918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rabphilin-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6827
Polymers18,5791
Non-polymers1,1036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.520, 92.520, 40.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 18579.307 Da / Num. of mol.: 2 / Fragment: C2B domain, UNP Residues 536-680
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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Non-polymers , 5 types, 43 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.31 Å3/Da / Density % sol: 20.14 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→65.422 Å / Num. obs: 11782 / % possible obs: 98.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
iMOSFLMdata reduction
SCALAccp4idata scaling
PHASERccp4iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CM5

2cm5


Resolution: 2.5→65.422 Å / Cross valid method: FREE R-VALUE / σ(F): 98 / Phase error: 37.65 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2646 606 5.14 %
Rwork0.2515 --
obs0.271 11781 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→65.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 145 29 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022474
X-RAY DIFFRACTIONf_angle_d0.5923310
X-RAY DIFFRACTIONf_dihedral_angle_d7.0011455
X-RAY DIFFRACTIONf_chiral_restr0.042339
X-RAY DIFFRACTIONf_plane_restr0.003399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5074-2.75950.34621480.30722652X-RAY DIFFRACTION91
2.7595-3.15840.30811360.2982750X-RAY DIFFRACTION93
3.1584-3.97760.25531730.25322797X-RAY DIFFRACTION94
3.9776-28.76780.271410.24822881X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 118.9748 Å / Origin y: 20.3093 Å / Origin z: -49.0305 Å
111213212223313233
T0.2775 Å2-0.0298 Å2-0.01 Å2-0.2854 Å20.0091 Å2--0.0657 Å2
L0.0837 °20.0227 °20.115 °2-0.0741 °20.046 °2--0.1597 °2
S-0.006 Å °0.042 Å °-0.008 Å °-0.0269 Å °0.0156 Å °0.0123 Å °0.0176 Å °-0.0203 Å °-0.0281 Å °
Refinement TLS groupSelection details: all

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