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- PDB-4mza: Crystal structure of hPIV3 hemagglutinin-neuraminidase -

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Basic information

Entry
Database: PDB / ID: 4mza
TitleCrystal structure of hPIV3 hemagglutinin-neuraminidase
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE / viral envelope protein / viral fusion protein
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman parainfluenza 3 virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.653 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: MBio / Year: 2013
Title: Interaction between the hemagglutinin-neuraminidase and fusion glycoproteins of human parainfluenza virus type III regulates viral growth in vivo.
Authors: Xu, R. / Palmer, S.G. / Porotto, M. / Palermo, L.M. / Niewiesk, S. / Wilson, I.A. / Moscona, A.
History
DepositionSep 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _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_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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,08819
Polymers97,6112
Non-polymers4,47717
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-16 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.782, 94.839, 105.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-neuraminidase


Mass: 48805.387 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 136-572)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parainfluenza 3 virus / Strain: Wash/47885/57 / Gene: HN / Plasmid: pFastbac-HT / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08492, exo-alpha-sialidase

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Sugars , 5 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h3-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 1
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
#5: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 2
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 , 5 types, 561 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 26% PEG1000, 0.1 M phosphate-citrate, pH 4.2, 0.1 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2010
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Number: 552524 / Rmerge(I) obs: 0.048 / Χ2: 1.03 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 100727 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555099.310.0310.9245.4
2.823.5599.810.0410.9835.8
2.462.8299.710.0531.0185.3
2.242.4699.810.071.0245.8
2.082.2499.610.0921.0865.2
1.962.0899.710.1341.0885.5
1.861.9699.810.2051.0835.7
1.781.8699.710.3431.0575.2
1.711.7899.610.4871.0015.4
1.651.7199.710.6921.0315.5
ReflectionResolution: 1.65→50 Å / Num. obs: 100727 / % possible obs: 99.7 %
Reflection shellHighest resolution: 1.65 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.653→47.42 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8715 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 5027 4.99 %
Rwork0.1665 --
obs0.1681 100646 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.63 Å2 / Biso mean: 31.0154 Å2 / Biso min: 9.78 Å2
Refinement stepCycle: LAST / Resolution: 1.653→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6813 0 288 550 7651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077323
X-RAY DIFFRACTIONf_angle_d1.2510020
X-RAY DIFFRACTIONf_chiral_restr0.0811184
X-RAY DIFFRACTIONf_plane_restr0.0051233
X-RAY DIFFRACTIONf_dihedral_angle_d20.6982807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.653-1.67170.26651530.23413131328499
1.6717-1.69140.25181770.219331473324100
1.6914-1.7120.25041760.218331593335100
1.712-1.73370.25731910.212731123303100
1.7337-1.75650.29371610.216331633324100
1.7565-1.78060.27781600.214631443304100
1.7806-1.8060.23151580.202131533311100
1.806-1.8330.24661610.187831683329100
1.833-1.86160.21381570.18631953352100
1.8616-1.89210.21451620.177131633325100
1.8921-1.92480.2231690.181331423311100
1.9248-1.95980.23821640.17131663330100
1.9598-1.99750.22461660.175531753341100
1.9975-2.03820.21751660.168731783344100
2.0382-2.08260.19021500.164331653315100
2.0826-2.1310.22441670.163431753342100
2.131-2.18430.20031640.17423172333699
2.1843-2.24340.21181800.173231593339100
2.2434-2.30940.20331630.167631813344100
2.3094-2.38390.20791660.172132023368100
2.3839-2.46910.21141640.16931913355100
2.4691-2.5680.20341590.171531893348100
2.568-2.68480.22411820.174931983380100
2.6848-2.82630.22441570.17283205336299
2.8263-3.00340.21521980.172531983396100
3.0034-3.23520.18841590.16432303389100
3.2352-3.56070.15561700.153232253395100
3.5607-4.07570.16921630.14623260342399
4.0757-5.1340.16011810.13193256343799
5.134-47.4390.20151830.18423417360099
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)
10.47230.3467-0.45482.6088-0.44091.04050.0761-0.2282-0.00260.3251-0.2636-0.337-0.08970.30270.1650.2238-0.0172-0.03640.29170.04670.186326.58085.19922.3225
22.35550.1732-0.5672.0176-0.31173.5480.08-0.35160.18280.3577-0.2098-0.115-0.60770.1540.13330.2756-0.1013-0.030.19990.01570.189628.754419.54813.2872
31.64621.0781-0.18342.89681.29642.16520.14670.22810.2884-0.2054-0.1472-0.2454-0.61220.18370.04220.316-0.07430.0010.10460.08330.189527.213320.8679-4.7952
42.28821.25860.69382.16160.08231.9427-0.12520.2885-0.0393-0.28030.04930.1146-0.0348-0.11870.05930.13750.04640.03050.1674-0.00680.104716.47615.5445-6.32
51.20050.1819-0.17691.3193-0.37221.9398-0.0112-0.02170.04940.0675-0.0587-0.0292-0.05680.0270.04710.09380.00280.00050.07160.00980.089819.02763.902210.0157
63.8987-0.02270.83414.2405-0.47162.89930.20070.31150.4064-0.2982-0.1612-0.3421-0.46360.2238-0.02370.2967-0.01690.05850.20590.03920.184430.003448.133822.7516
73.0041-0.0963-0.33774.454-0.6493.542-0.06850.0625-0.2293-0.1956-0.06940.02650.3606-0.02950.10190.18160.0261-0.01880.1543-0.07250.165525.821426.653629.514
82.69560.3868-0.66252.8554-0.29013.8579-0.065-0.1985-0.23290.11220.0359-0.23750.4110.19330.02360.13780.0455-0.04490.1852-0.01640.193431.799928.80848.1381
95.2448-3.84620.31963.6793-1.69443.2768-0.2468-0.57180.19910.26740.22150.15850.0547-0.01130.07120.2390.0054-0.00810.375-0.10180.24813.650543.900560.0687
102.9148-0.06770.3572.4614-0.58682.5317-0.062-0.22880.08890.07090.062-0.3197-0.11590.37460.01140.1068-0.0057-0.02710.212-0.06750.199630.776440.145648.3717
111.953-0.204-0.26641.38820.29052.23260.04590.01240.0941-0.1074-0.0776-0.0006-0.1582-0.13560.02880.15730.0382-0.01090.1209-0.02590.17316.129542.388435.6116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 141:194)A141 - 194
2X-RAY DIFFRACTION2chain 'A' and (resseq 195:270)A195 - 270
3X-RAY DIFFRACTION3chain 'A' and (resseq 271:314)A271 - 314
4X-RAY DIFFRACTION4chain 'A' and (resseq 315:376)A315 - 376
5X-RAY DIFFRACTION5chain 'A' and (resseq 377:572)A377 - 572
6X-RAY DIFFRACTION6chain 'B' and (resseq 138:171)B138 - 171
7X-RAY DIFFRACTION7chain 'B' and (resseq 172:247)B172 - 247
8X-RAY DIFFRACTION8chain 'B' and (resseq 248:340)B248 - 340
9X-RAY DIFFRACTION9chain 'B' and (resseq 341:376)B341 - 376
10X-RAY DIFFRACTION10chain 'B' and (resseq 377:423)B377 - 423
11X-RAY DIFFRACTION11chain 'B' and (resseq 424:572)B424 - 572

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  • 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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