[English] 日本語
Yorodumi
- PDB-4v11: Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v11
TitleStructure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
Components
  • SYNAPTIC VESICLE GLYCOPROTEIN 2A
  • SYNAPTOTAGMIN-1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / spontaneous neurotransmitter secretion ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / dense core granule / Toxicity of botulinum toxin type A (botA) / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / vesicle docking / regulation of exocytosis / exocytic vesicle / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle organization / protein heterooligomerization / positive regulation of dendrite extension / vesicle fusion / positive regulation of dopamine secretion / Glutamate Neurotransmitter Release Cycle / calcium-dependent phospholipid binding / neurotransmitter secretion / neuron projection terminus / membraneless organelle assembly / syntaxin-1 binding / Neurexins and neuroligins / low-density lipoprotein particle receptor binding / clathrin binding / synaptic vesicle priming / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / presynaptic active zone / excitatory synapse / transmembrane transporter activity / detection of calcium ion / postsynaptic cytosol / positive regulation of synaptic transmission / presynaptic cytosol / regulation of synaptic transmission, glutamatergic / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / SNARE binding / hippocampal mossy fiber to CA3 synapse / clathrin-coated endocytic vesicle membrane / molecular condensate scaffold activity / neuromuscular junction / GABA-ergic synapse / intracellular calcium ion homeostasis / calcium-dependent protein binding / synaptic vesicle membrane / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / cell-cell junction / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / lipid binding / calcium ion binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Synaptotagmin / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily / Major Facilitator Superfamily / C2 domain ...: / SV2A/B/C luminal domain / Synaptic vesicle protein SV2 / Synaptotagmin / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily / Major Facilitator Superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-1 / Synaptic vesicle glycoprotein 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / vanAalten, D.M.F. ...Zhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / vanAalten, D.M.F. / Cousin, M.A. / Alessi, D.R.
CitationJournal: J.Neurosci. / Year: 2015
Title: Phosphorylation of Synaptic Vesicle Protein 2A at Thr84 by Casein Kinase 1 Family Kinases Controls the Specific Retrieval of Synaptotagmin-1.
Authors: Zhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D.G. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / Van Aalten, D.M.F. / Cousin, M.A. / Alessi, D.R.
History
DepositionSep 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SYNAPTOTAGMIN-1
B: SYNAPTIC VESICLE GLYCOPROTEIN 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4636
Polymers18,2512
Non-polymers2124
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-40.1 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.049, 41.432, 48.014
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SYNAPTOTAGMIN-1 / SYNAPTOTAGMIN I / SYTI / P65


Mass: 17094.957 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN, UNP RESIDUES 273-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P-1 TEVB SYT1 270-END / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Protein/peptide SYNAPTIC VESICLE GLYCOPROTEIN 2A / SV2A


Mass: 1155.944 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 81-90 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7L0J3
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 81-90 WITH PHOSPHORYLATED T84

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.71 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 994 CCD-DETECTOR / Detector: CCD / Date: Mar 17, 2014 / Details: VARIMAX CU-VHF OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→31.28 Å / Num. obs: 13172 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 10.04 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 58.93
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 23.39 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TJX

1tjx


Resolution: 1.95→31.279 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 687 5.2 %
Rwork0.1512 --
obs0.1534 13172 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.9 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 9 147 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071315
X-RAY DIFFRACTIONf_angle_d1.0041774
X-RAY DIFFRACTIONf_dihedral_angle_d13.146502
X-RAY DIFFRACTIONf_chiral_restr0.046198
X-RAY DIFFRACTIONf_plane_restr0.004224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10060.19381270.12912383X-RAY DIFFRACTION95
2.1006-2.31190.22111610.14322480X-RAY DIFFRACTION100
2.3119-2.64630.18091300.15932502X-RAY DIFFRACTION100
2.6463-3.33340.21581380.15922525X-RAY DIFFRACTION100
3.3334-31.28260.17421310.15392595X-RAY DIFFRACTION100

+
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://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