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- PDB-8hr0: The complex structure of COPII coat with HCoV-OC43 DD sorting motif -

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Basic information

Entry
Database: PDB / ID: 8hr0
TitleThe complex structure of COPII coat with HCoV-OC43 DD sorting motif
Components
  • HCoV-OC43Human coronavirus OC43
  • Protein transport protein Sec23AProtein targeting
  • Protein transport protein Sec24AProtein targeting
  • Vesicle-trafficking protein SEC22b
KeywordsTRANSPORT PROTEIN / HCoV-OC43 / Spike / COPII vesicle / DD sorting motif
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / regulation of cholesterol transport / COPII-coated vesicle cargo loading / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / 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 / COPII vesicle coat / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / 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-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / transport vesicle / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / cholesterol homeostasis / protein localization to plasma membrane / 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 / phagocytic vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / ER-Phagosome pathway / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain ...Vesicle-trafficking protein Sec22 / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal / 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 / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus OC43
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsMa, W.F. / Nan, Y.N. / Yang, M.R. / Li, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
Beijing University of Chinese Medicine (BUCM)90011451310011, 1000061223476, ZYYCXTD-C-202006 China
CitationJournal: To Be Published
Title: Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations
Authors: Li, Y.Q. / Yang, M.R. / Nan, Y.N. / Wang, J.M. / Guo, J.J. / He, P.F. / Dai, W.X. / Zhou, S.Q. / Wang, S.J. / Zhang, Y. / Ma, W.F.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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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: HCoV-OC43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,9846
Polymers194,8534
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-21 kcal/mol
Surface area66140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.580, 96.203, 130.465
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein transport protein Sec23A / Protein targeting / hSec23A / SEC23-related protein A


Mass: 86249.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / Protein targeting / SEC24-related protein A


Mass: 84761.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O95486
#3: Protein Vesicle-trafficking protein SEC22b / ER-Golgi SNARE of 24 kDa / ERS-24 / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 ...ER-Golgi SNARE of 24 kDa / ERS-24 / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1


Mass: 22683.959 Da / Num. of mol.: 1
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 HCoV-OC43 / Human coronavirus OC43


Mass: 1158.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human coronavirus OC43
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 281.15 K / Method: evaporation / Details: 50 mM Tris-HCl, pH 7.9, 0.2 M NaAc and 16% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. obs: 26475 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.6
Reflection shellResolution: 3.34→3.45 Å / Num. unique obs: 2430 / CC1/2: 0.716

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Processing

Software
NameVersionClassification
PHENIX1.16.3549refinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→49.023 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 1994 7.53 %
Rwork0.2228 --
obs0.2286 26475 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→49.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12399 0 2 0 12401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112720
X-RAY DIFFRACTIONf_angle_d1.34417246
X-RAY DIFFRACTIONf_dihedral_angle_d5.0187748
X-RAY DIFFRACTIONf_chiral_restr0.0651948
X-RAY DIFFRACTIONf_plane_restr0.0082230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3401-3.42360.34931380.26591746X-RAY DIFFRACTION97
3.4236-3.51610.36881430.25711729X-RAY DIFFRACTION99
3.5161-3.61950.35691410.26431752X-RAY DIFFRACTION100
3.6195-3.73630.36511450.2581766X-RAY DIFFRACTION99
3.7363-3.86980.3481390.25841761X-RAY DIFFRACTION99
3.8698-4.02470.30411400.24561734X-RAY DIFFRACTION98
4.0247-4.20780.30981330.22681644X-RAY DIFFRACTION93
4.2078-4.42950.29811480.22821760X-RAY DIFFRACTION100
4.4295-4.70680.29061440.21011763X-RAY DIFFRACTION100
4.7068-5.06980.27671430.20491774X-RAY DIFFRACTION100
5.0698-5.57940.27071470.20551782X-RAY DIFFRACTION100
5.5794-6.38530.30381450.22181755X-RAY DIFFRACTION99
6.3853-8.0390.31441390.21391739X-RAY DIFFRACTION96
8.039-490.23381490.1831776X-RAY DIFFRACTION97

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