[English] 日本語
Yorodumi
- PDB-1epu: X-RAY crystal structure of neuronal SEC1 from squid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1epu
TitleX-RAY crystal structure of neuronal SEC1 from squid
ComponentsS-SEC1
KeywordsENDOCYTOSIS/EXOCYTOSIS / PARALLEL BETA-SHEETS / LEFT-HAND TURN CONNECTION / HELICAL BUNDLE / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


vesicle-mediated transport
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesLoligo pealei (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / TWO-WAVELENGTH MAD / Resolution: 2.4 Å
AuthorsBracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis.
Authors: Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-ray Analysis of Squid Neuronal Sec1
Authors: Bracher, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
History
DepositionMar 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Data collection
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-SEC1


Theoretical massNumber of molelcules
Total (without water)68,8151
Polymers68,8151
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.063, 121.989, 69.046
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein S-SEC1


Mass: 68815.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Cellular location: GIANT AXON / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O62547
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.94 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: batch crystallization / pH: 7.4
Details: Hepes, potassium chloride, dithiothreitol, pH 7.4, BATCH CRYSTALLIZATION, temperature 277K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Details: Bracher, A., (2000) Acta Crystallogr., Sect.D, 56, 501.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG10001reservoir
20.4 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir
420 mMdithiothreitol1reservoir
510 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 34634 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 55.95 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4042 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 116511
Reflection shell
*PLUS
% possible obs: 99.2 %

-
Processing

Software
NameClassification
SnBphasing
SHARPphasing
DMMultimodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMMultiphasing
RefinementMethod to determine structure: TWO-WAVELENGTH MAD / Resolution: 2.4→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1542 -RANDOM
Rwork0.24 ---
all0.2508 30751 --
obs0.2508 30601 99.5 %-
Displacement parametersBiso mean: 67.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 0 69 4481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d22.36
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.262
X-RAY DIFFRACTIONc_scangle_it2.032.5
LS refinement shellResolution: 2.4→2.43 Å / Total num. of bins used: 30 /
RfactorNum. reflection
Rfree0.414 55
Rwork0.347 949
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 29059
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.36
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

+
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