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- PDB-3eh2: Crystal structure of the human COPII-coat protein Sec24c -

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Basic information

Entry
Database: PDB / ID: 3eh2
TitleCrystal structure of the human COPII-coat protein Sec24c
ComponentsProtein transport protein Sec24CProtein targeting
KeywordsPROTEIN TRANSPORT / COPII-coat protein / vesicle transport / Cytoplasm / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Phosphoprotein / Transport
Function / homology
Function and homology information


COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / SNARE binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / SNARE binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / in utero embryonic development / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 Sec24C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 Sec24C
B: Protein transport protein Sec24C
C: Protein transport protein Sec24C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,0696
Polymers256,8733
Non-polymers1963
Water4,324240
1
A: Protein transport protein Sec24C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6902
Polymers85,6241
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein transport protein Sec24C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6902
Polymers85,6241
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein transport protein Sec24C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6902
Polymers85,6241
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.690, 182.980, 201.830
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 Sec24C / Protein targeting / SEC24-related protein C


Mass: 85624.172 Da / Num. of mol.: 3 / Fragment: conserved core, UNP residues 329-1094
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53992
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN VIA THE HANGING-DROP METHOD, BY ADDING 1UL PROTEIN SOLUTION TO 1UL OF WELL SOLUTION COMPRISING 6% (W/V) PEG 4000 AND 0.1 M MES., pH 7.5, 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: 2.3→50 Å / Num. obs: 104257 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.8
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→41.78 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 5212 RANDOM
Rwork0.241 --
obs-104257 -
Refinement stepCycle: LAST / Resolution: 2.35→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17547 0 3 240 17790

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