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- PDB-3eh1: Crystal structure of the human COPII-coat protein Sec24b -

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Basic information

Entry
Database: PDB / ID: 3eh1
TitleCrystal structure of the human COPII-coat protein Sec24b
ComponentsProtein transport protein Sec24B
KeywordsPROTEIN TRANSPORT / COPII coat protein / vesicle transport / transport signal sequence / Cytoplasm / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Phosphoprotein / Transport
Function / homology
Function and homology information


regulation of establishment of planar polarity involved in neural tube closure / regulation of cargo loading into COPII-coated vesicle / pulmonary artery morphogenesis / aorta morphogenesis / cochlear nucleus development / COPII-coated vesicle cargo loading / lung lobe morphogenesis / COPII vesicle coat / COPII vesicle coating / coronary artery morphogenesis ...regulation of establishment of planar polarity involved in neural tube closure / regulation of cargo loading into COPII-coated vesicle / pulmonary artery morphogenesis / aorta morphogenesis / cochlear nucleus development / COPII-coated vesicle cargo loading / lung lobe morphogenesis / COPII vesicle coat / COPII vesicle coating / coronary artery morphogenesis / Regulation of cholesterol biosynthesis by SREBP (SREBF) / antigen processing and presentation of peptide antigen via MHC class I / Cargo concentration in the ER / auditory receptor cell stereocilium organization / COPII-mediated vesicle transport / outflow tract morphogenesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / neural tube closure / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Golgi membrane / endoplasmic reticulum membrane / zinc ion binding / cytosol
Similarity search - Function
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 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 / Gelsolin-like domain superfamily / 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 Sec24B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 11, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein transport protein Sec24B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5282
Polymers84,4631
Non-polymers651
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.370, 67.500, 72.440
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein transport protein Sec24B / SEC24-related protein B


Mass: 84462.789 Da / Num. of mol.: 1 / Fragment: conserved core, UNP residues 518-1268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95487
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein was concentrated to 40 mg/ml in 150 mM NaCl, 20 mM Tris pH 7.5, 4 mM DTT. Crystals were grown via the hanging-drop method, by adding 1ul protein solution to 1ul of well solution ...Details: Protein was concentrated to 40 mg/ml in 150 mM NaCl, 20 mM Tris pH 7.5, 4 mM DTT. Crystals were grown via the hanging-drop method, by adding 1ul protein solution to 1ul of well solution comprising 42% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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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: 1.8→50 Å / Num. obs: 65527 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 / % possible all: 85

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.218 3276 random
Rwork0.184 --
obs-65527 -
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 1 691 6506

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