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- PDB-2beq: Structure of a Proteolytically Resistant Core from the Severe Acu... -

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Basic information

Entry
Database: PDB / ID: 2beq
TitleStructure of a Proteolytically Resistant Core from the Severe Acute Respiratory Syndrome Coronavirus S2 Fusion Protein
Components(Spike glycoproteinSpike protein) x 2
KeywordsVIRAL PROTEIN / COILED COIL / MEMBRANE FUSION / SARS / VIRAL ENTRY / ENVELOPE PROTEIN / GLYCOPROTEIN / TRANSMEMBRANE / VIRULENCE
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / 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 / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Single helix bin / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 helix bin / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 speciesHuman SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsSupekar, V.M. / Bruckmann, C. / Ingallinella, P. / Bianchi, E. / Pessi, A. / Carfi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of a Proteolytically Resistant Core from the Severe Acute Respiratory Syndrome Coronavirus S2 Fusion Protein
Authors: Supekar, V.M. / Bruckmann, C. / Ingallinella, P. / Bianchi, E. / Pessi, A. / Carfi, A.
History
DepositionNov 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 15, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_database_status / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Spike glycoprotein
E: Spike glycoprotein
F: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)27,2626
Polymers27,2626
Non-polymers00
Water3,639202
1
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Spike glycoprotein
E: Spike glycoprotein
F: Spike glycoprotein

A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Spike glycoprotein
E: Spike glycoprotein
F: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)54,52312
Polymers54,52312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area31830 Å2
ΔGint-244.9 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.907, 42.903, 59.826
Angle α, β, γ (deg.)90.00, 116.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 3869.315 Da / Num. of mol.: 3 / Fragment: RESIDUES 914-949 / Source method: obtained synthetically
Details: N-TERMINAL CAPPED WITH ACETYL GROUP BUT ONLY VISIBLE DENSITY ON B, C, D AND F. C-TERMINAL A, B, C, D, E, F CAPPED WITH AMINE GROUP
Source: (synth.) Human SARS coronavirus / References: UniProt: P59594
#2: Protein/peptide Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 5217.883 Da / Num. of mol.: 3 / Fragment: RESIDUES 1148-1193 / Source method: obtained synthetically
Details: N-TERMINAL CAPPED WITH ACETYL GROUP BUT ONLY VISIBLE DENSITY ON B, C, D AND F. C-TERMINAL A, B, C, D, E, F CAPPED WITH AMINE GROUP
Source: (synth.) Human SARS coronavirus / References: UniProt: P59594
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: STRUCTURAL PROTEIN THAT MAKES SPIKES AT THE SURFACE OF THE VIRUS.

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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: 2.1 Å3/Da / Density % sol: 35 %
Crystal growpH: 6.5
Details: 30% PEG8K, PH 7.0 100MM SODIUM CACODYLATE PH 6.5, 200MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 28450 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 93.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
ARP/wARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.43 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY WAS PRESENT FOR LEU1148 SIDE CHAIN ON CHAIN E AND FOR THE N-TERMINAL CAPPING ACETYL GROUPS OF CHAINS A AND E. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY WAS PRESENT FOR LEU1148 SIDE CHAIN ON CHAIN E AND FOR THE N-TERMINAL CAPPING ACETYL GROUPS OF CHAINS A AND E. THE CORRESPONDING ATOMS WERE NOT INCLUDED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1521 5.1 %RANDOM
Rwork0.199 ---
obs0.201 28450 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å21.39 Å2
2--1.53 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 0 202 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211902
X-RAY DIFFRACTIONr_bond_other_d0.0030.021750
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9812566
X-RAY DIFFRACTIONr_angle_other_deg1.50334114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2655239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02276
X-RAY DIFFRACTIONr_nbd_refined0.2930.2462
X-RAY DIFFRACTIONr_nbd_other0.2440.21976
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.51221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02421964
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2043681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5864.5602
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 98
Rwork0.329 2048

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