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- PDB-8tzu: OC43 S1b domain in complex with WNb 293 and WNb 317 -

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Basic information

Entry
Database: PDB / ID: 8tzu
TitleOC43 S1b domain in complex with WNb 293 and WNb 317
Components
  • Spike protein S1
  • WNb 293
  • WNb 317
KeywordsVIRAL PROTEIN / Antibody / SARS-CoV-2 Spike / Complex
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / carbohydrate binding / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...: / endocytosis involved in viral entry into host cell / carbohydrate binding / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / : / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / : / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHuman coronavirus OC43
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPymm, P. / Feng, J. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2021267 Australia
CitationJournal: To Be Published
Title: OC43 S1b domain in complex with WNb 293 and WNb 317
Authors: Pymm, P. / Feng, J. / Tham, W.H.
History
DepositionAug 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: WNb 317
D: WNb 293
E: WNb 293
F: Spike protein S1
G: WNb 317
H: WNb 317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,34217
Polymers157,3978
Non-polymers2,9459
Water1,20767
1
A: Spike protein S1
E: WNb 293
G: WNb 317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5977
Polymers57,1103
Non-polymers1,4874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint13 kcal/mol
Surface area23500 Å2
MethodPISA
2
B: Spike protein S1
C: WNb 317
D: WNb 293
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1437
Polymers57,1103
Non-polymers1,0334
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint1 kcal/mol
Surface area22970 Å2
MethodPISA
3
F: Spike protein S1
H: WNb 317
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6023
Polymers43,1782
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-1 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.914, 150.610, 155.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 3 molecules ABF

#1: Protein Spike protein S1


Mass: 29993.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus OC43 / Gene: S, 3 / Production host: Homo sapiens (human) / References: UniProt: P36334

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Antibody , 2 types, 5 molecules CGHDE

#2: Antibody WNb 317


Mass: 13183.584 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli K-12 (bacteria)
#3: Antibody WNb 293


Mass: 13932.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli K-12 (bacteria)

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Sugars , 3 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 71 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 23% PEG 1500, 0.1 M MMT pH 4.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.46 Å / Num. obs: 52029 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 78.81 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3.06 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7476 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.46 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 2621 5.04 %
Rwork0.2271 --
obs0.229 52029 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10781 0 139 67 10987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211170
X-RAY DIFFRACTIONf_angle_d0.53915152
X-RAY DIFFRACTIONf_dihedral_angle_d13.6863954
X-RAY DIFFRACTIONf_chiral_restr0.0431665
X-RAY DIFFRACTIONf_plane_restr0.0041961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.35111470.33332529X-RAY DIFFRACTION100
2.95-3.010.35571410.31422585X-RAY DIFFRACTION100
3.01-3.070.41231140.32492571X-RAY DIFFRACTION100
3.07-3.140.38281610.36322538X-RAY DIFFRACTION100
3.14-3.210.37631430.33242560X-RAY DIFFRACTION100
3.21-3.290.33261440.28932577X-RAY DIFFRACTION100
3.29-3.380.31571200.25042566X-RAY DIFFRACTION100
3.38-3.480.28961530.25052553X-RAY DIFFRACTION100
3.48-3.590.29941340.24722609X-RAY DIFFRACTION100
3.59-3.720.29061200.25462588X-RAY DIFFRACTION100
3.72-3.870.28871420.26042578X-RAY DIFFRACTION100
3.87-4.040.26131490.20992563X-RAY DIFFRACTION100
4.04-4.260.21441310.19142620X-RAY DIFFRACTION100
4.26-4.520.23511380.1752620X-RAY DIFFRACTION100
4.52-4.870.21311310.17832616X-RAY DIFFRACTION100
4.87-5.360.22871350.18022620X-RAY DIFFRACTION100
5.36-6.140.2551610.19652627X-RAY DIFFRACTION100
6.14-7.730.22541310.20582679X-RAY DIFFRACTION100
7.73-49.460.25161260.24072809X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.122 Å / Origin y: 32.9892 Å / Origin z: -9.1493 Å
111213212223313233
T0.4483 Å2-0.0594 Å20.0397 Å2-0.4912 Å20.0256 Å2--0.5049 Å2
L0.407 °2-0.2689 °20.2266 °2-0.4237 °2-0.1722 °2--0.7596 °2
S-0.0582 Å °0.1082 Å °0.0434 Å °0.1048 Å °-0.1041 Å °-0.0925 Å °-0.0871 Å °0.0445 Å °0.1657 Å °
Refinement TLS groupSelection details: all

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