[English] 日本語
Yorodumi
- PDB-1dqv: CRYSTAL STRUCTURE OF SYNAPTOTAGMIN III C2A/C2B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dqv
TitleCRYSTAL STRUCTURE OF SYNAPTOTAGMIN III C2A/C2B
ComponentsSYNAPTOTAGMIN III
KeywordsENDOCYTOSIS/EXOCYTOSIS / beta sandwich / calcium ion / C2 domain / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane / phosphatidylserine binding ...positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane / phosphatidylserine binding / synaptic vesicle exocytosis / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / synaptic membrane / response to calcium ion / presynapse / postsynapse / cell differentiation / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSutton, R.B. / Ernst, J.A. / Brunger, A.T.
CitationJournal: J.Cell Biol. / Year: 1999
Title: Crystal structure of the cytosolic C2A-C2B domains of synaptotagmin III. Implications for Ca(+2)-independent snare complex interaction.
Authors: Sutton, R.B. / Ernst, J.A. / Brunger, A.T.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SYNAPTOTAGMIN III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4476
Polymers33,2541
Non-polymers1935
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,78924
Polymers133,0164
Non-polymers77320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area9750 Å2
ΔGint-160 kcal/mol
Surface area53210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.959, 125.959, 118.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe biological assembly is one C2A domain and one C2B domain

-
Components

#1: Protein SYNAPTOTAGMIN III


Mass: 33253.914 Da / Num. of mol.: 1 / Fragment: C2A/C2B
Source method: isolated from a genetically manipulated source
Details: SOLUBLE PORTION / Source: (gene. exp.) Rattus rattus (black rat) / Organ: BRAIN / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P40748
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

-
Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Magnesium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
21.5 M1reservoirMgCl2
3100 mMMES1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 61080 / Num. obs: 9578 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: -1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 2.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.785 / Num. unique all: 929 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 61080
Reflection shell
*PLUS
% possible obs: 99.9 %

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used maximum likelihood/experiment phase set target function
RfactorNum. reflection% reflectionSelection details
Rfree0.3485 1564 -random
Rwork0.293 ---
all0.293 16371 --
obs0.293 16371 94.3 %-
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 9 0 2195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.622
X-RAY DIFFRACTIONc_bond_d0.0084
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.349
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.62
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.45 Å / Rfactor Rfree: 0.344 / Rfactor Rwork: 0.302

+
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