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- PDB-3i27: Structure of bovine torovirus Hemagglutinin-Esterase in complex w... -

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Basic information

Entry
Database: PDB / ID: 3i27
TitleStructure of bovine torovirus Hemagglutinin-Esterase in complex with receptor
ComponentsHemagglutinin-esterase
KeywordsHYDROLASE / SGNH-hydrolase fold / Swiss roll / Envelope protein / Glycoprotein / Hemagglutinin / Membrane / Transmembrane / Virion / Cell membrane
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / carbohydrate binding / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / 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
Chem-SID / Hemagglutinin-esterase
Similarity search - Component
Biological speciesBreda virus serotype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 29, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)177,70319
Polymers171,0994
Non-polymers6,60415
Water18,2311012
1
A: Hemagglutinin-esterase
B: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,66010
Polymers85,5502
Non-polymers3,1108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint35 kcal/mol
Surface area30550 Å2
MethodPISA
2
C: Hemagglutinin-esterase
D: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0449
Polymers85,5502
Non-polymers3,4947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint38 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.630, 112.890, 273.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Non-polymers , 2 types, 1016 molecules ABCD

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


Mass: 42774.805 Da / Num. of mol.: 4 / Fragment: residues 15-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Breda virus serotype 1 / Strain: Breda virus serotype 1 / Gene: HE / Plasmid: S1-Ig / Cell line (production host): HEK293S cell line / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: P0C0V9, sialate O-acetylesterase
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 15 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 5
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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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
#6: Sugar ChemComp-SID / methyl 9-S-acetyl-5-acetamido-3,5-dideoxy-9-thio-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 9-S-acetyl-5-(acetylamino)-3,5-dideoxy-9-thio-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / 5-N-acetyl-9-S-acetyl-9-thioneuraminic acid methyl glycoside / methyl 9-S-acetyl-5-acetamido-3,5-dideoxy-9-thio-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 9-S-acetyl-5-acetamido-3,5-dideoxy-9-thio-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 9-S-acetyl-5-acetamido-3,5-dideoxy-9-thio-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide / Mass: 381.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H23NO9S

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Details

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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium malonate, 0.1M Bis-Tris propane, pH 8.5, 25% (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: ID23-1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 141526 / Num. obs: 141525 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / Num. unique all: 20262 / % possible all: 98.6

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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 3I26

3i26


Resolution: 2→48.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.202 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21004 7106 5 %RANDOM
Rwork0.17864 ---
obs0.1802 134416 99.42 %-
all-141522 --
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: 15.257 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.132 Å-
Luzzati sigma a-0.093 Å
Refinement stepCycle: LAST / Resolution: 2→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11419 0 435 1012 12866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212266
X-RAY DIFFRACTIONr_bond_other_d0.0010.028101
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.99116784
X-RAY DIFFRACTIONr_angle_other_deg0.9663.00719602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10251450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15824.275517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.209151774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1381532
X-RAY DIFFRACTIONr_chiral_restr0.1450.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022466
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_it0.621.57278
X-RAY DIFFRACTIONr_mcbond_other0.1611.52904
X-RAY DIFFRACTIONr_mcangle_it1.098211845
X-RAY DIFFRACTIONr_scbond_it1.86434988
X-RAY DIFFRACTIONr_scangle_it2.9524.54939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 535 -
Rwork0.234 9711 -
obs-10232 98.04 %
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)
10.2670.25180.14240.9120.38480.4330.01040.00440.0002-0.0774-0.00770.0331-0.02070.0104-0.00270.02070.0226-0.02240.0482-0.04210.037711.26753.3103-27.5227
20.59540.22640.09290.92880.39320.52680.0841-0.0567-0.04490.0842-0.044-0.03380.07040.0091-0.04010.02080.0017-0.01530.0382-0.01670.0181-13.62260.2142-9.0149
31.1812-0.8194-0.01381.5024-0.07930.77850.08820.15780.0162-0.4179-0.1706-0.02340.00170.1730.08240.2310.0487-0.0460.1416-0.02240.049618.225153.6103-65.5011
40.2944-0.33240.03351.3699-0.09740.3069-0.01730.00480.0087-0.0778-0.03130.0107-0.01770.0290.04860.02210.0136-0.0190.0249-0.01590.02715.579348.8261-34.8342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 384
2X-RAY DIFFRACTION2B16 - 379
3X-RAY DIFFRACTION3C16 - 378
4X-RAY DIFFRACTION4D16 - 384

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