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- PDB-5zuv: Crystal Structure of the Human Coronavirus 229E HR1 motif in comp... -

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Basic information

Entry
Database: PDB / ID: 5zuv
TitleCrystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1
ComponentsSpike glycoprotein,Spike glycoprotein,inhibitor EK1
KeywordsVIRAL PROTEIN / INHIBITOR / Human Coronavirus 229E / Spike protein / S2 domain / HR1 motif / pan-Coronavirus
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Similarity search - Domain/homology
Biological speciesHuman coronavirus 229E
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 8, 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 / Structure summary
Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
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 1.3Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein,Spike glycoprotein,inhibitor EK1
B: Spike glycoprotein,Spike glycoprotein,inhibitor EK1
C: Spike glycoprotein,Spike glycoprotein,inhibitor EK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1425
Polymers44,0713
Non-polymers712
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-122 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.515, 45.548, 94.737
Angle α, β, γ (deg.)90.00, 96.33, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23C
14B
24C
15B
25C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUAA788 - 9155 - 132
21GLNGLNLEULEUBB788 - 9155 - 132
12LEULEUARGARGAA787 - 8684 - 85
22LEULEUARGARGCC787 - 8684 - 85
13ASPASPLEULEUAA882 - 91599 - 132
23ASPASPLEULEUCC882 - 91599 - 132
14GLNGLNARGARGBB788 - 8685 - 85
24GLNGLNARGARGCC788 - 8685 - 85
15ASPASPLEULEUBB882 - 91599 - 132
25ASPASPLEULEUCC882 - 91599 - 132

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Spike glycoprotein,Spike glycoprotein,inhibitor EK1 / S glycoprotein / E2 / Peplomer protein


Mass: 14690.345 Da / Num. of mol.: 3 / Fragment: UNP residues 785-873
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.) Human coronavirus 229E, (gene. exp.) synthetic construct (others)
Gene: S, 2 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P15423
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 0.05M MgCl2, 0.1M HEPES, pH 7.5, 30% PEG550MME

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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-F / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.21→44.4 Å / Num. obs: 20441 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.04 / Rrim(I) all: 0.087 / Net I/σ(I): 18.9
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 4.5 % / Num. unique obs: 1954 / Rpim(I) all: 0.097 / Rrim(I) all: 0.217 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.10.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bez

2bez


Resolution: 2.21→31.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24809 1020 5 %RANDOM
Rwork0.2019 ---
obs0.2042 19426 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.831 Å2
Baniso -1Baniso -2Baniso -3
1-5.52 Å20 Å21.44 Å2
2---1.89 Å2-0 Å2
3----3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.21→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 2 110 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9574007
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3925374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08727.333150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29915568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.673158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0393.9871508
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0755.9551878
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3194.4961462
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.90433.3414486
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3280.12
12B3280.12
21A2240.07
22C2240.07
31A640.02
32C640.02
41B2200.11
42C2200.11
51B600.01
52C600.01
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 69 -
Rwork0.245 1313 -
obs--91.34 %

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