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

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Basic information

Entry
Database: PDB / ID: 3efo
TitleCrystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of syntaxin 5
Components
  • Peptide
  • Protein transport protein Sec23A
  • SEC24 related gene family, member D
KeywordsPROTEIN TRANSPORT / COPII / coat protein / transport signal / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / Golgi disassembly / regulation of Golgi organization / early endosome to Golgi transport / Intra-Golgi traffic / COPII-coated vesicle cargo loading / vesicle docking / SNAP receptor activity / SNARE complex / COPII vesicle coat ...vesicle fusion with Golgi apparatus / Golgi disassembly / regulation of Golgi organization / early endosome to Golgi transport / Intra-Golgi traffic / COPII-coated vesicle cargo loading / vesicle docking / SNAP receptor activity / SNARE complex / COPII vesicle coat / vesicle fusion / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / RHOC GTPase cycle / endoplasmic reticulum exit site / RHOG GTPase cycle / RHOA GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / endomembrane system / 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 / positive regulation of protein catabolic process / vesicle / in utero embryonic development / cadherin binding / 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 / cytosol
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 / Protein transport protein Sec23 / Sec23, C-terminal / : / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type ...Syntaxin-5, N-terminal, Sly1p-binding domain / Syntaxin-5 N-terminal, Sly1p-binding domain / 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 / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Gelsolin-like domain superfamily / 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 / 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
Protein transport protein Sec24D / Syntaxin-5 / Protein transport protein Sec23A / Protein transport protein Sec24D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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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)173,7505
Polymers173,6193
Non-polymers1312
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-16 kcal/mol
Surface area61380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.060, 140.830, 152.250
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: 86177.367 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: 793.949 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of this 7-residue synthetic peptide occurs naturally in humans
References: UniProt: Q13190*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.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 5.5% (w/v) PEG 4000, 0.1 M magnesium sulfate and 100 mM HEPES, 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, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 58392 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2920 -random
Rwork0.211 ---
obs-58392 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11775 0 2 150 11927

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