[English] 日本語
Yorodumi
- PDB-3eg9: Crystal structure of the mammalian COPII-coat protein Sec23/24 bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eg9
TitleCrystal structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of membrin
Components
  • Protein transport protein Sec23A
  • SEC24 related gene family, member D
  • peptide
KeywordsPROTEIN TRANSPORT / COPII coat / vesicle transport / transport signal sequence / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / Intra-Golgi traffic / Golgi to vacuole transport / COPII-coated vesicle cargo loading / SNARE complex / SNAP receptor activity / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / intra-Golgi vesicle-mediated transport ...vesicle fusion with Golgi apparatus / Intra-Golgi traffic / Golgi to vacuole transport / COPII-coated vesicle cargo loading / SNARE complex / SNAP receptor activity / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / intra-Golgi vesicle-mediated transport / protein targeting to vacuole / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / IRE1-mediated unfolded protein response / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / late endosome membrane / in utero embryonic development / membrane => GO:0016020 / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / Golgi apparatus / zinc ion binding / membrane / cytosol
Similarity search - Function
GOSR2/Membrin/Bos1 / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain ...GOSR2/Membrin/Bos1 / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / SNARE / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Golgi SNAP receptor complex member 2 / Protein transport protein Sec24D / Protein transport protein Sec23A / Protein transport protein Sec24D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 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 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Protein transport protein Sec23A
B: SEC24 related gene family, member D
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,7215
Polymers173,5903
Non-polymers1312
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area61620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.130, 140.750, 152.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein transport protein Sec23A / 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 SEC24 related gene family, member D


Mass: 86647.852 Da / Num. of mol.: 1 / Fragment: conserved core, UNP residues 267-1033
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IYI7, UniProt: O94855*PLUS
#3: Protein/peptide peptide


Mass: 763.857 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of this 7-residue synthetic peptide occurs naturally in humans
References: UniProt: O14653*PLUS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
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, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 43252 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3EFO

3efo


Resolution: 3→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 593 random
Rwork0.202 --
obs-43252 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11847 0 2 107 11956

+
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