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- PDB-6lvn: Structure of the 2019-nCoV HR2 Domain -

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Basic information

Entry
Database: PDB / ID: 6lvn
TitleStructure of the 2019-nCoV HR2 Domain
ComponentsSpike protein S2'
KeywordsVIRAL PROTEIN / 2019-nCoV / 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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsZhu, Y. / Sun, F.
CitationJournal: To Be Published
Title: Crystal structure of HR2 domain of 2019-nCoV S2 subunit
Authors: Zhu, Y. / Sun, F.
History
DepositionFeb 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct / struct_ref / struct_ref_seq
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.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description
Revision 1.4Nov 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'
B: Spike protein S2'
C: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)16,0464
Polymers16,0464
Non-polymers00
Water39622
1
A: Spike protein S2'
C: Spike protein S2'

B: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)16,0464
Polymers16,0464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area5670 Å2
ΔGint-57 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.195, 49.729, 89.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein/peptide
Spike protein S2' / Spike protein S2


Mass: 4011.470 Da / Num. of mol.: 4 / Fragment: HR2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris HCl, pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.469→26.894 Å / Num. obs: 4862 / % possible obs: 99.22 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.1324 / Net I/σ(I): 19.06
Reflection shellResolution: 2.47→2.558 Å / Num. unique obs: 456 / CC1/2: 0.939

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYY

1wyy


Resolution: 2.47→25.6 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.258 --
Rwork0.2148 --
obs-4862 99.26 %
Displacement parametersBiso mean: 38.51 Å2
Refinement stepCycle: LAST / Resolution: 2.47→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 22 1078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451052
X-RAY DIFFRACTIONf_angle_d0.72631416
X-RAY DIFFRACTIONf_chiral_restr0.0494180
X-RAY DIFFRACTIONf_plane_restr0.0043188
X-RAY DIFFRACTIONf_dihedral_angle_d16.7333672
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)
10.90350.0203-0.82220.3116-0.8207-0.0340.01870.2239-0.1741-0.2627-0.0740.33570.1329-0.0070.00120.29020.0031-0.03780.2319-0.03660.246610.596732.917328.9788
20.12570.88270.80110.22220.39790.22150.2256-0.2823-0.05370.347-0.2752-0.13520.05640.013900.23070.01830.020.262-0.02340.28925.285437.546861.3536
30.0338-0.3453-0.30590.024-0.45140.6601-0.0711-0.26-0.1189-0.1480.1617-0.01260.05410.06420.00020.2857-0.0445-0.01160.2438-0.05530.246716.106428.771940.3969
41.21470.09691.04660.71260.76221.54440.3677-0.12340.31790.65411.17660.5614-0.2469-0.37690.47080.2677-0.02220.18940.5010.15220.5372-0.296145.496634.2446
50.28950.06940.00340.2373-0.25361.0068-0.02060.3528-0.05190.39810.22290.10580.0946-0.27140.02320.2999-0.01470.03360.2176-0.01760.271-0.39230.007951.4449
61.33530.3081.47750.33470.42361.81050.17320.08320.4272-1.03240.1259-0.40640.1102-0.43441.36510.31510.02230.12380.4072-0.00760.506816.481848.646352.0183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A2 - 35
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 36 )B2 - 36
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 26 )C3 - 26
4X-RAY DIFFRACTION4chain 'C' and (resid 27 through 35 )C27 - 35
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 26 )D2 - 26
6X-RAY DIFFRACTION6chain 'D' and (resid 27 through 35 )D27 - 35

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