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- PDB-6m1v: Crystal structure of post fusion core of 2019-nCoV S2 subunit -

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Basic information

Entry
Database: PDB / ID: 6m1v
TitleCrystal structure of post fusion core of 2019-nCoV S2 subunit
ComponentsSpike protein S2,Spike protein S2
KeywordsVIRAL PROTEIN / 2019-nCoV / spike protein / fusion core
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
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 ...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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSun, H. / Song, H. / Wang, Q.
CitationJournal: Emerg Microbes Infect / Year: 2020
Title: Structural basis of HCoV-19 fusion core and an effective inhibition peptide against virus entry.
Authors: Sun, H. / Li, Y. / Liu, P. / Qiao, C. / Wang, X. / Wu, L. / Liu, K. / Hu, Y. / Su, C. / Tan, S. / Zou, S. / Wu, G. / Yan, J. / Gao, G.F. / Qi, J. / Wang, Q.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _entity.pdbx_description / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Spike protein S2,Spike protein S2


Theoretical massNumber of molelcules
Total (without water)12,6941
Polymers12,6941
Non-polymers00
Water2,036113
1
A: Spike protein S2,Spike protein S2

A: Spike protein S2,Spike protein S2

A: Spike protein S2,Spike protein S2


Theoretical massNumber of molelcules
Total (without water)38,0823
Polymers38,0823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8120 Å2
ΔGint-70 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.666, 42.666, 106.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1358-

HOH

21A-1409-

HOH

31A-1410-

HOH

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Components

#1: Protein Spike protein S2,Spike protein S2


Mass: 12694.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P0DTC2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-tris, pH 6.5, and 25% (wt/vol) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 18825 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.1 % / Biso Wilson estimate: 13.72 Å2 / CC1/2: 1 / Net I/σ(I): 49
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1838 / CC1/2: 0.996 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNC

1wnc


Resolution: 1.5→21.62 Å / SU ML: 0.1516 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 836 4.7 %
Rwork0.2034 16950 -
obs0.2038 17786 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 0 113 806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053715
X-RAY DIFFRACTIONf_angle_d0.7011970
X-RAY DIFFRACTIONf_chiral_restr0.06121
X-RAY DIFFRACTIONf_plane_restr0.0041129
X-RAY DIFFRACTIONf_dihedral_angle_d20.0458271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.590.2574860.23132018X-RAY DIFFRACTION68.38
1.59-1.720.26181540.23882868X-RAY DIFFRACTION98.44
1.72-1.890.22411380.22122938X-RAY DIFFRACTION100
1.89-2.160.2321570.20192971X-RAY DIFFRACTION99.97
2.16-2.720.18741440.19472984X-RAY DIFFRACTION100
2.72-21.620.20271570.19513171X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: -6.74288234371 Å / Origin y: 26.817114098 Å / Origin z: 134.433542038 Å
111213212223313233
T0.0471395688726 Å20.00711487979862 Å2-0.00158850712178 Å2-0.0943740517257 Å20.000805022748077 Å2--0.133653971599 Å2
L0.513003074959 °20.0670110944365 °2-0.0816415126423 °2-0.498351653822 °20.161797203483 °2--2.52263345462 °2
S-0.00582629660946 Å °0.0723519125849 Å °0.0199586874067 Å °-0.0467899964191 Å °-0.0396156424113 Å °0.0783713786641 Å °-0.0501943107361 Å °-0.574578546613 Å °0.0637876483025 Å °
Refinement TLS groupSelection details: all

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