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- PDB-3eg9: Crystal structure of the mammalian COPII-coat protein Sec23/24 bo... -

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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


Intra-Golgi traffic / COPII-coated vesicle cargo loading / COPII vesicle coat / XBP1(S) activates chaperone genes / SNARE complex / SNAP receptor activity / vesicle fusion / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / intra-Golgi vesicle-mediated transport ...Intra-Golgi traffic / COPII-coated vesicle cargo loading / COPII vesicle coat / XBP1(S) activates chaperone genes / SNARE complex / SNAP receptor activity / vesicle fusion / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / intra-Golgi vesicle-mediated transport / COPII-mediated vesicle transport / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / 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 / protein transport / in utero embryonic development / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / Golgi apparatus / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
GOSR2/Membrin/Bos1 / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / 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 ...GOSR2/Membrin/Bos1 / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / 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 / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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