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- PDB-3egd: Crystal structure of the mammalian COPII-coat protein Sec23a/24a ... -

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Basic information

Entry
Database: PDB / ID: 3egd
TitleCrystal structure of the mammalian COPII-coat protein Sec23a/24a complexed with the SNARE protein Sec22 and bound to the transport signal sequence of vesicular stomatitis virus glycoprotein
Components
  • (Protein transport protein ...) x 2
  • 10 residue peptide from VSV glycoprotein
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / COPII coat / transport signal sequence / vesicle / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / COPII vesicle coat / 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 exit site / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / protein localization to plasma membrane / cholesterol homeostasis / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / phagocytic vesicle membrane / melanosome / protein transport / ER-Phagosome pathway / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / perinuclear region of cytoplasm / zinc ion binding / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain ...Vesicle-trafficking protein Sec22 / Longin domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / 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 / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / Beta-Lactamase / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Glycoprotein / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Protein transport protein Sec24A
C: Vesicle-trafficking protein SEC22b
D: 10 residue peptide from VSV glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,9616
Polymers189,8304
Non-polymers1312
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-15 kcal/mol
Surface area66680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.750, 97.630, 129.120
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein transport protein ... , 2 types, 2 molecules AB

#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 Protein transport protein Sec24A / 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

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Protein / Protein/peptide , 2 types, 2 molecules CD

#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 domain, 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 10 residue peptide from VSV glycoprotein


Mass: 1283.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic 10-residue peptide / References: UniProt: P03522*PLUS

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Non-polymers , 2 types, 165 molecules

#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
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

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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, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 46345 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 2317 random
Rwork0.206 --
all-999 -
obs-46345 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12589 0 2 163 12754

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