[English] 日本語
Yorodumi
- PDB-7u4q: Human Synaptotagmin-1 C2A Y181F Ca2+ bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u4q
TitleHuman Synaptotagmin-1 C2A Y181F Ca2+ bound
ComponentsSynaptotagmin-1
KeywordsEXOCYTOSIS / C2 domain / AD3 / C2A / Greek Key / synaptotagmin
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 / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway ...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 / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / clathrin-sculpted monoamine transport vesicle membrane / dense core granule / chromaffin granule membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / vesicle docking / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / positive regulation of dendrite extension / regulation of exocytosis / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / syntaxin binding / low-density lipoprotein particle receptor binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / cellular response to calcium ion / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsDominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1R21MH070589-01 United States
CitationJournal: To Be Published
Title: Human Synaptotagmin-1 C2A Y181F Ca2+ bound
Authors: Dominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synaptotagmin-1
B: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7095
Polymers30,5892
Non-polymers1203
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.810, 99.810, 77.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 15294.448 Da / Num. of mol.: 2 / Fragment: C2A domain / Mutation: Y181F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 100 mM HEPES, 2.3 M malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 81798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 81798 Å / Relative weight: 1
ReflectionResolution: 1.56→26.06 Å / Num. obs: 53881 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 27.28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04023 / Rpim(I) all: 0.01098 / Rrim(I) all: 0.04172 / Net I/σ(I): 27.72
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.899 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 5347 / CC1/2: 0.434 / CC star: 0.778 / Rpim(I) all: 0.6487 / Rrim(I) all: 2.013 / % possible all: 99.63

-
Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
xia2data scaling
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wee

4wee


Resolution: 1.56→26.06 Å / SU ML: 0.1841 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1888 1991 3.7 %
Rwork0.1638 51861 -
obs0.1648 53852 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.59 Å2
Refinement stepCycle: LAST / Resolution: 1.56→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 3 233 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112216
X-RAY DIFFRACTIONf_angle_d1.2533003
X-RAY DIFFRACTIONf_chiral_restr0.0903317
X-RAY DIFFRACTIONf_plane_restr0.0059394
X-RAY DIFFRACTIONf_dihedral_angle_d13.7883831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.33671370.31763664X-RAY DIFFRACTION99.61
1.6-1.640.28171440.26273712X-RAY DIFFRACTION99.77
1.64-1.690.2561420.21453673X-RAY DIFFRACTION100
1.69-1.750.26711380.20223691X-RAY DIFFRACTION99.97
1.75-1.810.24191410.21223673X-RAY DIFFRACTION99.92
1.81-1.880.23641430.19563699X-RAY DIFFRACTION99.95
1.88-1.970.19091410.15243706X-RAY DIFFRACTION99.92
1.97-2.070.19391430.14393664X-RAY DIFFRACTION100
2.07-2.20.18581410.14753707X-RAY DIFFRACTION99.97
2.2-2.370.20521410.14233731X-RAY DIFFRACTION100
2.37-2.610.19711460.14473730X-RAY DIFFRACTION100
2.61-2.980.2121420.18653710X-RAY DIFFRACTION99.97
2.98-3.760.16731440.16413717X-RAY DIFFRACTION100
3.76-26.060.16431480.15173784X-RAY DIFFRACTION99.87

+
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