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- PDB-3cl5: Structure of coronavirus hemagglutinin-esterase in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 3cl5
TitleStructure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid
ComponentsHemagglutinin-esterase
KeywordsHYDROLASE / SGNH-hydrolase fold / Swiss roll / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


negative regulation of immune system process / sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / signaling receptor binding / viral envelope ...negative regulation of immune system process / sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / signaling receptor binding / viral envelope / host cell plasma membrane / virion membrane / protein homodimerization activity / identical protein binding / membrane
Similarity search - Function
Hemagglutinin-esterase / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
ACETIC ACID / : / Chem-SIO / Hemagglutinin-esterase
Similarity search - Component
Biological speciesBovine coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZeng, Q.H. / Langereis, M.A. / van Vliet, A.L.W. / Huizinga, E.G. / de Groot, R.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution.
Authors: Zeng, Q. / Langereis, M.A. / van Vliet, A.L. / Huizinga, E.G. / de Groot, R.J.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66710
Polymers42,6301
Non-polymers2,0379
Water5,062281
1
A: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,33420
Polymers85,2602
Non-polymers4,07418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6730 Å2
ΔGint39.1 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 89.240, 280.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin-esterase / HE protein / E3 glycoprotein


Mass: 42630.230 Da / Num. of mol.: 1 / Fragment: residues 19-388 / Mutation: S40A
Source method: isolated from a genetically manipulated source
Details: HEK293S cell line / Source: (gene. exp.) Bovine coronavirus / Strain: Mebus / Gene: HE / Plasmid: S1-Ig / Production host: Homo Sapiens (human) / References: UniProt: P15776, sialate O-acetylesterase

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Sugars , 3 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-SIO / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide, alpha linking / Mass: 407.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H25NO11

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Non-polymers , 3 types, 283 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (w/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.8→77.4 Å / Num. all: 60345 / Num. obs: 60283 / % possible obs: 97.2 % / Observed criterion σ(I): -3.7 / Redundancy: 20.7 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 19 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7667 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
DNAdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type structure of Hemagglutinin-esterase

Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.463 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 3043 5.1 %RANDOM
Rwork0.17031 ---
obs0.1712 57018 96.05 %-
all-57018 --
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: 25.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 131 281 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223086
X-RAY DIFFRACTIONr_bond_other_d0.0010.021988
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9744217
X-RAY DIFFRACTIONr_angle_other_deg1.2823.0054776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99424.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9251511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
X-RAY DIFFRACTIONr_mcbond_it0.6251.51784
X-RAY DIFFRACTIONr_mcbond_other0.1641.5723
X-RAY DIFFRACTIONr_mcangle_it1.13422883
X-RAY DIFFRACTIONr_scbond_it1.85831302
X-RAY DIFFRACTIONr_scangle_it2.9744.51334
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 197 -
Rwork0.237 3250 -
obs--76.7 %
Refinement TLS params.Method: refined / Origin x: 5.4113 Å / Origin y: 33.4158 Å / Origin z: 12.5268 Å
111213212223313233
T-0.0348 Å2-0.0087 Å2-0.0106 Å2--0.022 Å2-0.0268 Å2---0.0455 Å2
L0.7643 °2-0.1215 °20.1801 °2-0.3569 °20.0688 °2--0.5919 °2
S0 Å °0.0312 Å °-0.0714 Å °-0.0298 Å °0.0127 Å °0.0263 Å °0.1292 Å °-0.0626 Å °-0.0127 Å °

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