[English] 日本語
Yorodumi
- PDB-5low: Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 comple... -

+
Open data


ID or keywords:

Loading...

-
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 / BLOC-1 complex / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / synaptic vesicle fusion to presynaptic active zone membrane ...selenium binding / BLOC-1 complex / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / synaptic vesicle fusion to presynaptic active zone membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / ribbon synapse / regulation of establishment of protein localization / calcium ion-regulated exocytosis of neurotransmitter / extrinsic component of synaptic vesicle membrane / regulation of calcium ion-dependent exocytosis / cholinergic synapse / SNARE complex / SNAP receptor activity / positive regulation of hormone secretion / neurotransmitter secretion / inositol 1,4,5 trisphosphate binding / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / extrinsic component of membrane / myosin binding / exocytosis / phosphate ion binding / voltage-gated potassium channel activity / synaptic vesicle exocytosis / associative learning / long-term memory / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / somatodendritic compartment / phosphatidylinositol-4,5-bisphosphate binding / photoreceptor inner segment / axonogenesis / SNARE binding / secretory granule / filopodium / locomotory behavior / long-term synaptic potentiation / intracellular protein transport / neuromuscular junction / neuron differentiation / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / phospholipid binding / synaptic vesicle membrane / small GTPase binding / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / presynapse / lamellipodium / presynaptic membrane / cell cortex / growth cone / postsynapse / postsynaptic membrane / transmembrane transporter binding / dendritic spine / cytoskeleton / endosome / neuron projection / protein domain specific binding / axon / neuronal cell body / glutamatergic synapse / lipid binding / synapse / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family ...Rabphilin-3A / : / Rabphilin/DOC2/Noc2 / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / 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 / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more