[English] 日本語
Yorodumi
- PDB-7tx9: Human Synaptotagmin-1 C2B Y312F Ca2+ bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tx9
TitleHuman Synaptotagmin-1 C2B Y312F Ca2+ bound
ComponentsSynaptotagmin
KeywordsEXOCYTOSIS / C2 domain / AD3 / C2B / Greek Key / synaptotagmin
Function / homology
Function and homology information


chromaffin granule membrane / synaptic vesicle membrane / calcium ion binding
Similarity search - Function
Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Chem-1PG / Synaptotagmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 C2B Y312F Ca2+ bound
Authors: Dominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
History
DepositionFeb 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4349
Polymers17,8641
Non-polymers5708
Water2,162120
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)54.290, 54.290, 102.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Synaptotagmin


Mass: 17863.818 Da / Num. of mol.: 1 / Fragment: UNP Residues 269-419 / Mutation: Y312F
Source method: isolated from a genetically manipulated source
Details: orginally cloned from human brain cDNA library / Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SYT1, hCG_2016754 / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3KQA0

-
Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5,200 mM ammonium sulfate, 50% w/v PEG 2000MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09717 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09717 Å / Relative weight: 1
ReflectionResolution: 1.34→34.61 Å / Num. obs: 38659 / % possible obs: 96.38 % / Redundancy: 14.4 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06678 / Rpim(I) all: 0.01733 / Rrim(I) all: 0.06914 / Net I/σ(I): 24.3
Reflection shellResolution: 1.34→1.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3196 / CC1/2: 0.407 / CC star: 0.761 / Rpim(I) all: 0.8528 / Rrim(I) all: 1.519 / % possible all: 80.61

-
Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tz3

6tz3


Resolution: 1.34→34.61 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 2004 5.2 %
Rwork0.1693 36540 -
obs0.1703 38544 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.34→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 28 120 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921360
X-RAY DIFFRACTIONf_angle_d1.20131846
X-RAY DIFFRACTIONf_chiral_restr0.0864202
X-RAY DIFFRACTIONf_plane_restr0.0059235
X-RAY DIFFRACTIONf_dihedral_angle_d16.0316531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.37431110.37192085X-RAY DIFFRACTION77.96
1.37-1.410.37131300.35952398X-RAY DIFFRACTION89.74
1.41-1.450.34251380.32622599X-RAY DIFFRACTION97.3
1.45-1.50.25081480.24372642X-RAY DIFFRACTION99.32
1.5-1.550.26781500.2412637X-RAY DIFFRACTION98.38
1.55-1.610.32311340.31422542X-RAY DIFFRACTION95.13
1.61-1.690.18281460.16022689X-RAY DIFFRACTION99.96
1.69-1.780.26491370.23492511X-RAY DIFFRACTION93.5
1.78-1.890.16811510.13092676X-RAY DIFFRACTION99.61
1.89-2.030.17791470.1422670X-RAY DIFFRACTION99.02
2.03-2.240.12791530.10752722X-RAY DIFFRACTION99.9
2.24-2.560.16171450.11962739X-RAY DIFFRACTION99.79
2.56-3.230.1611530.15112738X-RAY DIFFRACTION99.48
3.23-34.610.1711610.16252892X-RAY DIFFRACTION99.77

+
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