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- PDB-8x5p: Crystal structure of MjHKUr-CoV spike HR1 in complex with EK1 peptide -

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Basic information

Entry
Database: PDB / ID: 8x5p
TitleCrystal structure of MjHKUr-CoV spike HR1 in complex with EK1 peptide
ComponentsSpike protein S2,EK1 peptide
KeywordsVIRAL PROTEIN / MjHKUr-CoV / spike protein / postfusion / VIRUS
Function / homology
Function and homology information


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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesCoronavirus HKU23
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsZhu, Y. / Yang, X. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Fusion mechanism of MjHKUr-CoV spike and its entry inhibitor
Authors: Zhu, Y. / Sun, F. / Lu, L.
History
DepositionNov 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S2,EK1 peptide
B: Spike protein S2,EK1 peptide
C: Spike protein S2,EK1 peptide
D: Spike protein S2,EK1 peptide
E: Spike protein S2,EK1 peptide
F: Spike protein S2,EK1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7258
Polymers71,6546
Non-polymers712
Water2,540141
1
A: Spike protein S2,EK1 peptide
B: Spike protein S2,EK1 peptide
C: Spike protein S2,EK1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8634
Polymers35,8273
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-96 kcal/mol
Surface area13030 Å2
MethodPISA
2
D: Spike protein S2,EK1 peptide
E: Spike protein S2,EK1 peptide
F: Spike protein S2,EK1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8634
Polymers35,8273
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-101 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.373, 42.344, 169.294
Angle α, β, γ (deg.)90.00, 98.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Spike protein S2,EK1 peptide


Mass: 11942.375 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronavirus HKU23 / Gene: S / Production host: Escherichia coli (E. coli) / References: UniProt: Q0Q4F2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate, Citric Acid pH 5.5, 20%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→29.61 Å / Num. obs: 17070 / % possible obs: 94.5 % / Redundancy: 4 % / CC1/2: 0.997 / Net I/σ(I): 14.6
Reflection shellResolution: 2.51→2.61 Å / Num. unique obs: 1922 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.61 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 858 5.04 %
Rwork0.2291 --
obs0.2318 17008 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 2 141 4440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.764
X-RAY DIFFRACTIONf_dihedral_angle_d3.674553
X-RAY DIFFRACTIONf_chiral_restr0.048701
X-RAY DIFFRACTIONf_plane_restr0.004744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.660.34071400.26322721X-RAY DIFFRACTION95
2.66-2.870.28211420.24392712X-RAY DIFFRACTION97
2.87-3.160.32861200.25422781X-RAY DIFFRACTION98
3.16-3.610.26211470.22552762X-RAY DIFFRACTION96
3.61-4.550.25321350.18672314X-RAY DIFFRACTION81
4.55-29.610.28831740.23642860X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7819-0.11230.21820.09670.52091.7199-0.0851-0.0575-0.03070.1377-0.0524-0.15480.07690.13360.00970.2154-0.0037-0.00530.11540.00390.17644.620528.526645.9158
20.9814-0.09790.29860.9722-0.25661.762-0.06690.0278-0.09670.0781-0.06420.0598-0.2133-0.3925-0.00830.1296-0.003-0.00660.04420.01110.2045-5.496930.573947.7022
30.4691-0.2713-0.11920.7415-0.47111.56420.03390.00320.0930.05180.07290.0556-0.63760.01230.00950.157-0.03220.0090.1215-0.00230.17971.012238.200846.359
40.332-0.2969-0.7030.4292-0.42991.26750.0857-0.036-0.03140.08990.08240.0373-0.2904-0.4580.03190.0808-0.03470.00320.1302-0.02770.165519.769535.016529.6208
50.25450.1677-0.41560.19060.70121.14730.0843-0.03170.01460.05190.08980.0332-0.11550.28020.1820.0836-0.0015-0.00170.07520.00050.105529.295134.978630.0731
60.2727-0.04070.12720.5366-0.36443.280.0884-0.00150.06290.06320.11510.01150.4567-0.16920.18580.101-0.0232-0.01220.09860.01170.136824.4126.807430.0065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 109)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 110)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 109)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 110)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 111)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 111)

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