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- PDB-6lxt: Structure of post fusion core of 2019-nCoV S2 subunit -

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Basic information

Entry
Database: PDB / ID: 6lxt
TitleStructure of post fusion core of 2019-nCoV S2 subunit
ComponentsSpike protein S2, Spike protein S2
KeywordsVIRAL PROTEIN / 2019-nCoV / HR1 and HR2 domain / VIRUS
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhu, Y. / Sun, F.
CitationJournal: Cell Res. / Year: 2020
Title: Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion.
Authors: Xia, S. / Liu, M. / Wang, C. / Xu, W. / Lan, Q. / Feng, S. / Qi, F. / Bao, L. / Du, L. / Liu, S. / Qin, C. / Sun, F. / Shi, Z. / Zhu, Y. / Jiang, S. / Lu, L.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.pdbx_descriptor
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,65814
Polymers83,8776
Non-polymers7818
Water0
1
A: Spike protein S2, Spike protein S2
B: Spike protein S2, Spike protein S2
C: Spike protein S2, Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5899
Polymers41,9393
Non-polymers6506
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-166 kcal/mol
Surface area16650 Å2
MethodPISA
2
D: Spike protein S2, Spike protein S2
E: Spike protein S2, Spike protein S2
F: Spike protein S2, Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0695
Polymers41,9393
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-139 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.240, 57.580, 115.720
Angle α, β, γ (deg.)90.000, 91.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Spike protein S2, Spike protein S2


Mass: 13979.517 Da / Num. of mol.: 6 / Fragment: HR1 domain,HR2 domain
Source method: isolated from a genetically manipulated source
Details: The fusion protein of SARS-CoV-2 S2 subunit HR1 domain (residues 910-988), linker (SGGRGG), SARS-CoV-2 S2 subunit HR2 domain (residues 1162-1206), and expression tag (GG)
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 8000, 200 mM zinc acetate, 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→47.32 Å / Num. obs: 14470 / % possible obs: 94.02 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.3
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.13 / Num. unique obs: 1518 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYY

1wyy


Resolution: 2.9→47.32 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2896 737 -
Rwork0.2593 --
obs-14313 94.02 %
Displacement parametersBiso mean: 87.99 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 32 0 5237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325236
X-RAY DIFFRACTIONf_angle_d1.93317058
X-RAY DIFFRACTIONf_chiral_restr0.0824883
X-RAY DIFFRACTIONf_plane_restr0.0047928
X-RAY DIFFRACTIONf_dihedral_angle_d16.58673277
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.43 --
Rwork0.36 --
obs-1518 99.02 %
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)
10.879-0.23742.05211.1830.77554.1848-0.1692-0.31970.11150.2142-0.27780.01951.46520.53550.34250.3209-0.1685-0.00960.4257-0.03960.56480.2412-8.3537-9.1105
21.99281.27960.53840.49560.10119.1352-0.5006-0.0024-0.42690.4437-0.47840.21692.8674-1.28020.52690.7199-0.00320.10540.3763-0.01260.6602-3.9445-13.0811-24.3006
31.41050.05271.58390.87581.0117.9196-0.0724-0.41840.3088-0.1111-0.31380.1401-0.7469-1.64010.24680.419-0.05440.0530.38420.00260.5413-2.8489-2.3518-7.4223
41.2663-0.59750.88391.8861-1.15435.6942-0.688-0.00160.6351-0.5283-0.17050.063-3.1416-0.81460.54870.59940.0362-0.0130.4770.00450.6502-3.64213.0534-22.6603
50.83030.37250.62410.49111.28722.8979-0.0301-0.04180.09850.1336-0.1594-0.0282-0.61611.25960.32380.39660.0610.01340.41510.02620.49083.5558-3.4281-7.7641
61.4698-0.42811.89932.8031.07946.7348-0.31570.41350.3039-0.7129-0.8618-0.70160.90323.66750.16340.44910.00490.04020.84650.11970.609110.5411-3.7654-27.7443
71.05030.0366-2.40720.6764-2.36015.34160.10830.26090.0225-0.0180.07370.0499-0.8793-2.2547-0.20050.54960.0491-0.02570.65880.03150.6621-27.956412.9843-8.7303
81.44021.0851-1.01441.6632-2.51072.0012-0.97561.1960.32850.35030.09440.5788-3.2079-2.6311-0.40471.12970.69430.05552.14030.0610.8141-32.900418.4936-25.5955
91.5723-0.0307-2.33680.31511.21314.17380.23280.0061-0.07790.14760.1336-0.0731-3.9636-0.38110.30210.9160.0439-0.05370.43080.08610.8038-22.496915.3056-10.2925
100.10750.0799-0.81680.003-0.70055.4676-0.0801-1.13310.42170.6631-0.8776-0.56420.43193.11470.39340.76740.082-0.05121.4555-0.12660.798-19.38623.977421.4824
112.5998-0.875-0.32470.58740.90952.0237-0.1468-0.12180.2669-0.1874-1.0854-0.7374-2.12922.35680.27531.0129-0.32910.07670.92670.11240.8279-14.578916.5574-24.1988
123.29940.9945-4.77070.339-1.48626.89030.13460.45520.88320.2967-0.0674-0.0058-4.78420.6360.07131.7061-0.0680.1311.27970.41520.7938-18.259223.3735-51.4769
130.6453-0.56670.19480.91421.72463.2852-0.3878-0.0581-0.1503-0.0588-0.3009-0.19111.7520.72670.3630.4212-0.0903-0.03120.3467-0.06290.6499-22.97248.1924-10.9034
140.36690.07530.0020.223-0.94345.1251-0.31870.6689-0.18340.07890.1234-0.07393.2181-2.26690.51230.9609-0.267-0.02250.6369-0.15650.7258-25.69363.5944-20.4859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 912 through 1167 )A912 - 1167
2X-RAY DIFFRACTION2chain 'A' and (resid 1168 through 1202 )A1168 - 1202
3X-RAY DIFFRACTION3chain 'B' and (resid 914 through 1165 )B914 - 1165
4X-RAY DIFFRACTION4chain 'B' and (resid 1166 through 1202 )B1166 - 1202
5X-RAY DIFFRACTION5chain 'C' and (resid 912 through 1171 )C912 - 1171
6X-RAY DIFFRACTION6chain 'C' and (resid 1172 through 1202 )C1172 - 1202
7X-RAY DIFFRACTION7chain 'D' and (resid 912 through 1174 )D912 - 1174
8X-RAY DIFFRACTION8chain 'D' and (resid 1175 through 1197 )D1175 - 1197
9X-RAY DIFFRACTION9chain 'E' and (resid 915 through 985 )E915 - 985
10X-RAY DIFFRACTION10chain 'E' and (resid 986 through 1174 )E986 - 1174
11X-RAY DIFFRACTION11chain 'E' and (resid 1175 through 1196 )E1175 - 1196
12X-RAY DIFFRACTION12chain 'E' and (resid 1197 through 1202 )E1197 - 1202
13X-RAY DIFFRACTION13chain 'F' and (resid 913 through 987 )F913 - 987
14X-RAY DIFFRACTION14chain 'F' and (resid 988 through 1202 )F988 - 1202

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