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- PDB-4c7w: Crystal structure of Mouse Hepatitis virus strain S Hemagglutinin... -

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Basic information

Entry
Database: PDB / ID: 4c7w
TitleCrystal structure of Mouse Hepatitis virus strain S Hemagglutinin- esterase in complex with 4-O-acetylated sialic acid
ComponentsHEMAGGLUTININ-ESTERASE
KeywordsHYDROLASE / RECEPTOR DESTROYING / RECEPTOR BINDING
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-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 / virion membrane / 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
: / Chem-SIO / Hemagglutinin-esterase / Hemagglutinin-esterase
Similarity search - Component
Biological speciesMURINE HEPATITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZeng, Q.H. / Huizinga, E.G.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Murine Coronavirus Hemagglutinin-Esterase Receptor-Binding Site: A Major Shift in Ligand Specificity Through Modest Changes in Architecture.
Authors: Langereis, M.A. / Zeng, Q. / Heesters, B.A. / Huizinga, E.G. / De Groot, R.J.
History
DepositionSep 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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_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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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 2.1Dec 20, 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 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,56919
Polymers87,0072
Non-polymers6,56217
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-31.3 kcal/mol
Surface area41440 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.566, 106.590, 135.607
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 , 1 types, 2 molecules AB

#1: Protein HEMAGGLUTININ-ESTERASE


Mass: 43503.355 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MURINE HEPATITIS VIRUS / Strain: S / Plasmid: PCD5- MHV-S-HE-T-FC / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human)
References: UniProt: O55252, UniProt: P31614*PLUS, sialate O-acetylesterase

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Sugars , 5 types, 14 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.: 4
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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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
#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-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.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H25NO11
#7: 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.: 4
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

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Non-polymers , 3 types, 78 molecules

#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 3.6
Details: 0.2 M KH2PO4, 0.2 M SODIUM MALONATE, 15% (W/V) PEG3350 AND 5% (W/V) GLYCEROL, pH 3.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→54.5 Å / Num. obs: 46670 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C7L

4c7l


Resolution: 2.5→83.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.042 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24877 2356 5.1 %RANDOM
Rwork0.21371 ---
obs0.21546 44251 99.97 %-
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: 45.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.78 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5441 0 426 75 5942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226071
X-RAY DIFFRACTIONr_bond_other_d0.0010.023975
X-RAY DIFFRACTIONr_angle_refined_deg1.2292.0268284
X-RAY DIFFRACTIONr_angle_other_deg0.86439585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64824.103273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8215854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.381522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021253
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_it0.5011.53425
X-RAY DIFFRACTIONr_mcbond_other0.0761.51390
X-RAY DIFFRACTIONr_mcangle_it0.96925502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77132646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2014.52782
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 183 -
Rwork0.308 3203 -
obs--100 %
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)
14.5911-1.86660.09274.17540.38982.50870.07340.41410.1231-1.08580.25940.54640.0568-0.2536-0.33280.3421-0.1527-0.20820.14290.11780.215-44.3717-29.90227.3419
22.75992.28753.74711.97933.13125.1409-0.62150.050.2954-0.69180.12040.3679-0.9261-0.03550.50110.4651-0.0518-0.18270.37440.10990.3356-42.8515-20.09320.8157
339.379626.1397-2.311821.6723-10.615419.2294-0.86021.5185-1.1749-0.90570.7869-0.78880.70480.38260.07320.3337-0.0202-0.01570.1632-0.02880.2246-33.9625-25.76261.1876
42.6830.523-0.53962.0843-0.31751.94760.08070.17750.4972-0.2081-0.0144-0.2239-0.37480.1921-0.06640.1338-0.02390.07560.0460.05230.1671-22.0123-7.18698.6741
546.696111.389619.87634.9085-0.455923.80940.05041.28540.2542-0.2243-0.0618-0.43220.15591.26520.01140.3353-0.12460.36360.48450.09160.9347-0.16690.30271.1663
61.3591-0.3539-0.46360.80890.23812.70340.1161-0.11130.5645-0.0090.0113-0.4004-0.45520.3379-0.12740.1117-0.0750.04630.0891-0.04490.3469-14.3223-8.393313.6592
74.41112.2429-0.44134.5327-0.55531.40310.099-0.03930.5687-0.02560.0040.1552-0.2495-0.0569-0.1030.0720.02540.03840.01450.0050.0874-29.8942-11.012815.8935
84.27141.38651.22657.96331.28390.4799-0.06291.2379-0.5912-0.35390.2887-0.83510.00020.3594-0.22580.15760.02950.0870.3732-0.14670.1543-30.3933-31.118811.1516
91.08172.2113-1.07125.8285-2.41821.1718-0.130.1754-0.0198-0.35390.23030.40630.2523-0.2526-0.10030.2034-0.1198-0.05860.26110.07510.2279-47.9453-45.959820.2232
108.64493.19592.00465.37120.96543.25260.0372-0.9806-0.01110.8001-0.10150.07440.37680.02650.06430.23780.04340.02160.25410.08360.0608-33.8691-39.484340.5188
112.12620.59610.76385.23181.84432.44650.1055-0.7633-0.33641.01860.0527-0.2720.40990.0557-0.15820.31490.0524-0.1260.45130.0320.1419-21.0242-31.177346.4766
122.47612.23291.557415.51878.30215.9104-0.0143-0.9254-0.00561.2384-0.14030.1431-0.0211-0.33130.15460.41740.1166-0.02490.4704-0.11660.1968-24.9792-14.047945.4483
131.52920.47120.42041.9217-0.05721.45770.0052-0.38840.30080.46030.0129-0.5061-0.37260.2934-0.0180.2487-0.0299-0.08860.315-0.15590.2935-12.9642-11.159537.0678
144.30631.1822-2.65360.6508-1.50683.767-0.0374-0.7470.17210.51560.00870.0838-1.1209-0.42880.02870.86390.2680.15850.6515-0.28310.244-35.3792-24.559239.078
153.26490.5794-1.36176.1092-1.09251.98490.0466-0.3876-0.19650.2445-0.08430.40730.3058-0.23240.03770.2014-0.04180.08750.27010.09510.1078-45.6691-44.208734.1012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 50
2X-RAY DIFFRACTION2A58 - 104
3X-RAY DIFFRACTION3A105 - 108
4X-RAY DIFFRACTION4A114 - 217
5X-RAY DIFFRACTION5A218 - 226
6X-RAY DIFFRACTION6A227 - 270
7X-RAY DIFFRACTION6A802
8X-RAY DIFFRACTION7A271 - 306
9X-RAY DIFFRACTION8A315 - 334
10X-RAY DIFFRACTION9A348 - 410
11X-RAY DIFFRACTION10B25 - 44
12X-RAY DIFFRACTION11B66 - 105
13X-RAY DIFFRACTION12B106 - 140
14X-RAY DIFFRACTION13B141 - 305
15X-RAY DIFFRACTION13B802
16X-RAY DIFFRACTION14B314 - 332
17X-RAY DIFFRACTION15B351 - 405

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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