[English] 日本語
Yorodumi
- PDB-1h3q: Crystal structure of SEDL at 2.4 Angstroms resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h3q
TitleCrystal structure of SEDL at 2.4 Angstroms resolution
ComponentsSEDLIN
KeywordsTRANSPORT / SEDL / SEDT / ENDOPLASMIC RETICULUM / GOLGI / VESICLE TRANSPORT
Function / homology
Function and homology information


vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport ...vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / COPII vesicle coating / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / transcription corepressor binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Beta-Lactamase - #70 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Trafficking protein particle complex subunit 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJang, S.B. / Kim, Y.-G. / Cho, Y.-S. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Sedl and its Implications for a Genetic Disease Spondyloepiphyseal Dysplasia Tarda
Authors: Jang, S.B. / Kim, Y.-G. / Cho, Y.-S. / Suh, P.-G. / Kim, K.-H. / Oh, B.-H.
History
DepositionSep 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SEDLIN


Theoretical massNumber of molelcules
Total (without water)16,4631
Polymers16,4631
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.690, 101.300, 66.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein SEDLIN / SEDL


Mass: 16462.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CQP2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY PLAY A ROLE IN VESICULAR TRANSPORT FROM ENDOPLASMIC RETICULUM TO GOLGI. MEMBER OF THE ...MAY PLAY A ROLE IN VESICULAR TRANSPORT FROM ENDOPLASMIC RETICULUM TO GOLGI. MEMBER OF THE TRAPP/SEDLIN SUBFAMILY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.361 Å3/Da / Density % sol: 47.9 %
Crystal growpH: 6.5
Details: 1.4M SODIUM ACETATE, 0.1M SODIUM CACODYLATE PH6.5, pH 6.50
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH7.6
2250 mM1dropNaCl
310 mg/mlprotein1drop
41.4 Msodium acetate1reservoir
50.1 Msodium cacodylate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97934,0.97947,0.97166
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979471
30.971661
ReflectionResolution: 2.4→30 Å / Num. obs: 6083 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Net I/σ(I): 24.2
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 6 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 33601 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.146

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -5 %RANDOM
Rwork0.213 ---
obs0.213 6081 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 0 24 1187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.236
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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