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- PDB-5zvk: Crystal Structure of the Human Coronavirus MERS HR1 motif in comp... -

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Basic information

Entry
Database: PDB / ID: 5zvk
TitleCrystal Structure of the Human Coronavirus MERS HR1 motif in complex with pan-CoVs inhibitor EK1
Components
  • Human Coronavirus MERS HR1 motif
  • pan-CoV inhibitory peptide EK1
KeywordsVIRAL PROTEIN/INHIBITOR / MERS / Spike protein / S2 domain / HR1 motif / pan-Coronavirus / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsYan, L. / Yang, B. / Wilson, I.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31600619 China
CitationJournal: Sci Adv / Year: 2019
Title: A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike.
Authors: Xia, S. / Yan, L. / Xu, W. / Agrawal, A.S. / Algaissi, A. / Tseng, C.K. / Wang, Q. / Du, L. / Tan, W. / Wilson, I.A. / Jiang, S. / Yang, B. / Lu, L.
History
DepositionMay 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 28, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Coronavirus MERS HR1 motif
B: Human Coronavirus MERS HR1 motif
C: Human Coronavirus MERS HR1 motif
a: pan-CoV inhibitory peptide EK1
b: pan-CoV inhibitory peptide EK1
c: pan-CoV inhibitory peptide EK1


Theoretical massNumber of molelcules
Total (without water)40,4556
Polymers40,4556
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-119 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 60.280, 175.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Human Coronavirus MERS HR1 motif


Mass: 8561.517 Da / Num. of mol.: 3 / Fragment: UNP residues 984-1062
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli (E. coli) / References: UniProt: W6A0A7, UniProt: K9N5Q8*PLUS
#2: Protein/peptide pan-CoV inhibitory peptide EK1


Mass: 4923.550 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The manually designed EK1 inhibitor was modified from a Coronavirus sequence (UNP P36334 SPIKE_CVHOC, UNP residues 1252-1288).
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Sequence detailsThe protein used for crystallization is a HR1-SGGRGG-EK1 fusion protein that contains MERS HR1 ...The protein used for crystallization is a HR1-SGGRGG-EK1 fusion protein that contains MERS HR1 motif, followed by SGGRGG linker, followed by manually designed EK1 peptide.

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 0.2M KSCN, pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.31→25.8 Å / Num. obs: 6009 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 109 Å2 / CC1/2: 0.897 / Rpim(I) all: 0.036 / Rrim(I) all: 0.122 / Net I/σ(I): 20.7
Reflection shellResolution: 3.31→3.43 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 564 / Rpim(I) all: 0.324 / Rrim(I) all: 0.775 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mod

4mod


Resolution: 3.31→25.8 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.17
RfactorNum. reflection% reflection
Rfree0.3136 339 5.69 %
Rwork0.259 --
obs0.2622 5953 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.31→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 0 0 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022356
X-RAY DIFFRACTIONf_angle_d0.5523163
X-RAY DIFFRACTIONf_dihedral_angle_d15.3961456
X-RAY DIFFRACTIONf_chiral_restr0.036378
X-RAY DIFFRACTIONf_plane_restr0.002408
LS refinement shellResolution: 3.31→3.43 Å / Rfactor Rfree: 0.318 / Rfactor Rwork: 0.34
Refinement TLS params.Method: refined / Origin x: 36.3284 Å / Origin y: 34.8555 Å / Origin z: 188.4057 Å
111213212223313233
T0.678 Å20.1873 Å20.0751 Å2-0.6651 Å20.1082 Å2--0.7339 Å2
L7.074 °2-3.7619 °2-2.5162 °2-3.4631 °21.5613 °2--2.4813 °2
S0.4311 Å °0.4167 Å °0.0777 Å °-0.3267 Å °-0.2002 Å °0.2979 Å °-0.5074 Å °-0.5441 Å °-0.201 Å °
Refinement TLS groupSelection details: all

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