[English] 日本語
Yorodumi
- PDB-3egx: Crystal structure of the mammalian COPII-coat protein Sec23a/24a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3egx
TitleCrystal structure of the mammalian COPII-coat protein Sec23a/24a complexed with the SNARE protein Sec22b and bound to the transport signal sequence of the SNARE protein Bet1
Components
  • 9-residue synthetic peptide from SNARE protein Bet1
  • Protein transport protein Sec23AProtein targeting
  • Protein transport protein Sec24AProtein targeting
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / COPII coat protein / vesicle transport / transport signal sequence / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / Golgi trans cisterna / regulation of cholesterol transport / COPII vesicle coating / COPII-coated vesicle cargo loading / integral component of Golgi membrane / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity ...vesicle fusion with Golgi apparatus / Golgi trans cisterna / regulation of cholesterol transport / COPII vesicle coating / COPII-coated vesicle cargo loading / integral component of Golgi membrane / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / extrinsic component of membrane / endoplasmic reticulum exit site / SNARE binding / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / transport vesicle / GTPase activator activity / cholesterol homeostasis / protein localization to plasma membrane / intracellular protein transport / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of protein secretion / positive regulation of protein catabolic process / ER to Golgi transport vesicle membrane / melanosome / phagocytic vesicle membrane / protein transport / ER-Phagosome pathway / endoplasmic reticulum-Golgi intermediate compartment / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / zinc ion binding / membrane / integral component of membrane / cytosol
Similarity search - Function
BET1-like protein / BET1, SNARE domain / Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Longin domain / beta-sandwich domain of Sec23/24 / Sec23/Sec24 helical domain ...BET1-like protein / BET1, SNARE domain / Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Longin domain / beta-sandwich domain of Sec23/24 / Sec23/Sec24 helical domain / Protein transport protein Sec23 / Sec23, C-terminal / Sec24-like, trunk domain / Sec23/Sec24 beta-sandwich / Sec23/Sec24, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, helical domain / Sec23/Sec24 zinc finger / Sec23/Sec24 helical domain / Sec23/Sec24 trunk domain / Sec23/Sec24 beta-sandwich domain / Sec23/Sec24 helical domain superfamily / Zn-finger domain of Sec23/24 / Zinc finger, Sec23/Sec24-type superfamily / Synaptobrevin / Synaptobrevin / Gelsolin-like domain superfamily / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Gelsolin-like domain / Gelsolin repeat / Severin / Severin / Longin-like domain superfamily / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Beta-Lactamase / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BET1 homolog / Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å
AuthorsGoldberg, J. / Mancias, J.D.
CitationJournal: Embo J. / Year: 2008
Title: Structural basis of cargo membrane protein discrimination by the human COPII coat machinery.
Authors: Mancias, J.D. / Goldberg, J.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24A
C: Vesicle-trafficking protein SEC22b
D: 9-residue synthetic peptide from SNARE protein Bet1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,6796
Polymers189,5484
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-20 kcal/mol
Surface area66210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.150, 97.230, 129.510
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein transport protein Sec23A / Protein targeting / SEC23-related protein A


Mass: 86178.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / Protein targeting / SEC24-related protein A


Mass: 84336.820 Da / Num. of mol.: 1 / Fragment: Conserved core, UNP residues 346-1093
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95486
#3: Protein Vesicle-trafficking protein SEC22b / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1 / ERS24 / ERS-24


Mass: 18031.645 Da / Num. of mol.: 1 / Fragment: cytoplasmic domainn, UNP residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC22B, SEC22L1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75396
#4: Protein/peptide 9-residue synthetic peptide from SNARE protein Bet1


Mass: 1000.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic 9-residue peptide / References: UniProt: O15155*PLUS
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 10% (w/v) PEG 4000, 0.1 M NaCl, 0.5 M sodium acetate, 50 mM Tris buffer, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 24079 / % possible obs: 92 % / Observed criterion σ(F): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.292 1204 random
Rwork0.206 --
obs-24079 -
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12521 0 2 0 12523

+
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