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- PDB-8x7x: Crystal structure of SADS-CoV fusion core -

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Basic information

Entry
Database: PDB / ID: 8x7x
TitleCrystal structure of SADS-CoV fusion core
Components
  • HR1
  • HR2
KeywordsVIRAL PROTEIN / fusion core / postfusion
Function / homology
Function and homology information


host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesCoronaviridae (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYan, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Viruses / Year: 2024
Title: Crystal Structures of Fusion Cores from CCoV-HuPn-2018 and SADS-CoV.
Authors: Wang, F. / Yang, G. / Yan, L.
History
DepositionNov 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: HR1
F: HR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0453
Polymers12,0092
Non-polymers351
Water37821
1
C: HR1
F: HR2
hetero molecules

C: HR1
F: HR2
hetero molecules

C: HR1
F: HR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1359
Polymers36,0286
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area17450 Å2
ΔGint-201 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.176, 45.176, 418.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-1005-

HOH

21C-1015-

HOH

31C-1016-

HOH

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Components

#1: Protein HR1


Mass: 8052.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronaviridae (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A8JNZ2
#2: Protein/peptide HR2


Mass: 3957.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronaviridae (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A8JP08
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1M HEPES pH 7.5, 42% PEG 200

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.59→28.56 Å / Num. obs: 5590 / % possible obs: 98.93 % / Redundancy: 1 % / CC1/2: 0.984 / Net I/σ(I): 2
Reflection shellResolution: 2.59→2.68 Å / Num. unique obs: 55 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→28.56 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 286 5.14 %
Rwork0.2351 --
obs0.2375 5568 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 1 21 825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007800
X-RAY DIFFRACTIONf_angle_d0.7791082
X-RAY DIFFRACTIONf_dihedral_angle_d23.386289
X-RAY DIFFRACTIONf_chiral_restr0.047139
X-RAY DIFFRACTIONf_plane_restr0.004141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-3.260.31511460.23342557X-RAY DIFFRACTION99
3.26-28.560.27331400.23562725X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -21.225 Å / Origin y: 8.5734 Å / Origin z: 20.4505 Å
111213212223313233
T0.4414 Å2-0.0064 Å2-0.0335 Å2-0.4371 Å20.0224 Å2--0.3702 Å2
L1.0288 °2-0.0783 °20.7872 °2-1.7179 °2-0.7536 °2--0.877 °2
S-0.0894 Å °-0.3424 Å °-0.1184 Å °0.2022 Å °0.0242 Å °0.0608 Å °0.9602 Å °0.3553 Å °0.1388 Å °
Refinement TLS groupSelection details: all

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