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- PDB-3i1l: Structure of porcine torovirus Hemagglutinin-Esterase in complex ... -

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Basic information

Entry
Database: PDB / ID: 3i1l
TitleStructure of porcine torovirus Hemagglutinin-Esterase in complex with its receptor
ComponentsHemagglutinin-esterase protein
KeywordsHYDROLASE / SGNH-hydrolase fold / Swiss roll / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


sialate O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / plasma membrane
Similarity search - Function
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 / sialate O-acetylesterase
Similarity search - Component
Biological speciesPorcine torovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsZeng, Q.H. / Huizinga, E.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for ligand and substrate recognition by torovirus hemagglutinin esterases
Authors: Langereis, M.A. / Zeng, Q.H. / Gerwig, G.J. / Frey, B. / von Itzstein, M. / Kamerling, J.P. / de Groot, R.J. / Huizinga, E.G.
History
DepositionJun 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: 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 / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 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 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin-esterase protein
B: Hemagglutinin-esterase protein
C: Hemagglutinin-esterase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,81525
Polymers125,8733
Non-polymers4,94222
Water19811
1
A: Hemagglutinin-esterase protein
hetero molecules

A: Hemagglutinin-esterase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,06216
Polymers83,9162
Non-polymers3,14714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5390 Å2
ΔGint31 kcal/mol
Surface area28750 Å2
MethodPISA
2
B: Hemagglutinin-esterase protein
C: Hemagglutinin-esterase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,28417
Polymers83,9162
Non-polymers3,36815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint33 kcal/mol
Surface area28920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.030, 103.690, 97.070
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin-esterase protein


Mass: 41957.773 Da / Num. of mol.: 3 / Fragment: residues 24-393 / Mutation: S46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine torovirus / Strain: Markelo / Gene: HE / Plasmid: S1-Ig / Cell line (production host): HEK293S cell line / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: Q70KP4, sialate O-acetylesterase
#2: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C16H25NO11
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: 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.: 16
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium acetate, 18% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.79→48 Å / Num. all: 36150 / Num. obs: 36150 / % possible obs: 94.3 % / Observed criterion σ(I): -3.7 / Redundancy: 2.7 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.5
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2 / Num. unique all: 5312 / % possible all: 95.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I1K

3i1k


Resolution: 2.79→46.27 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 29.554 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24285 1817 5 %RANDOM
Rwork0.19228 ---
obs0.1948 34330 93.78 %-
all-36147 --
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: 25.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.05 Å2
2---0.15 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati sigma a0.356 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.79→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8487 0 320 11 8818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.98112423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25851083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3724.286399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5671521
X-RAY DIFFRACTIONr_chiral_restr0.0740.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3061.55415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60828751
X-RAY DIFFRACTIONr_scbond_it1.15933702
X-RAY DIFFRACTIONr_scangle_it2.144.53672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.786→2.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 141 -
Rwork0.302 2530 -
obs-2671 94.55 %
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)
12.24520.3064-0.14954.4454-0.19061.6403-0.0169-0.14140.11080.1324-0.21960.4867-0.0755-0.22590.23660.06520.00020.010.193-0.06640.0986-13.641916.67896.9027
24.0736-1.4454-0.21973.15660.95091.5547-0.1155-0.08640.44860.26560.1009-0.2839-0.0351-0.00390.01460.1039-0.021-0.03310.0369-0.01260.0604-31.76931.052441.2142
34.6093-0.4494-0.05922.63910.83451.8989-0.12560.3168-0.22220.0711-0.04380.05670.2544-0.19510.16940.1722-0.09620.01980.0842-0.02840.0264-43.0521-23.825327.1484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 386
2X-RAY DIFFRACTION2B25 - 386
3X-RAY DIFFRACTION3C25 - 386

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