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- PDB-1pd0: Crystal structure of the COPII coat subunit, Sec24, complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1pd0
TitleCrystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Sed5 (yeast syntaxin-5)
Components
  • COPII-binding peptide of the integral membrane protein SED5
  • Protein transport protein Sec24
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of inclusion body assembly / RHOC GTPase cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / Golgi cis cisterna membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of ER to Golgi vesicle-mediated transport / COPI-mediated anterograde transport ...regulation of inclusion body assembly / RHOC GTPase cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / Golgi cis cisterna membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of ER to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / vesicle fusion / vesicle docking / COPII vesicle coat / SNARE complex / SNAP receptor activity / positive regulation of protein exit from endoplasmic reticulum / intra-Golgi vesicle-mediated transport / cis-Golgi network / signal sequence binding / fungal-type vacuole membrane / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / SNARE binding / macroautophagy / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / membrane
Similarity search - Function
Syntaxin-5, N-terminal, Sly1p-binding domain / Syntaxin-5 N-terminal, Sly1p-binding domain / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / : / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain ...Syntaxin-5, N-terminal, Sly1p-binding domain / Syntaxin-5 N-terminal, Sly1p-binding domain / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / : / 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 / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. / Gelsolin-like domain superfamily / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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
Protein transport protein SEC24 / Integral membrane protein SED5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMossessova, E. / Bickford, L.C. / Goldberg, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: SNARE selectivity of the COPII coat.
Authors: Mossessova, E. / Bickford, L.C. / Goldberg, J.
History
DepositionMay 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein Sec24
B: COPII-binding peptide of the integral membrane protein SED5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0953
Polymers92,0302
Non-polymers651
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.527, 94.527, 197.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein transport protein Sec24 / Abnormal nuclear morphology 1


Mass: 90841.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sec24 fragment lacking n-terminal residues 1-116 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40482
#2: Protein/peptide COPII-binding peptide of the integral membrane protein SED5


Mass: 1188.267 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE
References: UniProt: Q01590
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: sodium acetate 1,6-hexanediol, cobalt chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mg/mlprotein1drop
2200 mM1dropNaCl
320 mMHEPES1droppH7.3
44 mMdithiothreitol1drop
5100 mM1reservoirNaOAcpH5.8
60.35 M1,6-hexanediol1reservoir
74 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 30516 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.09 / Net I/σ(I): 30.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 6.6 / Num. unique all: 3001 / Rsym value: 0.09 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 73768
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 94.8 % / Num. unique obs: 3001 / Num. measured obs: 7154

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1755474.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1476 5.1 %RANDOM
Rwork0.206 ---
obs0.206 29148 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9592 Å2 / ksol: 0.36742 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.43 Å28.25 Å20 Å2
2--9.43 Å20 Å2
3----18.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 1 163 6063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2.6→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 70 4.4 %
Rwork0.306 1517 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / Num. reflection obs: 29162 / % reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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