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- PDB-4jf7: Structure of the parainfluenza virus 5 (PIV5) hemagglutinin-neura... -

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Basic information

Entry
Database: PDB / ID: 4jf7
TitleStructure of the parainfluenza virus 5 (PIV5) hemagglutinin-neuraminidase (HN) ectodomain
ComponentsHemagglutinin-neuraminidase
KeywordsVIRAL PROTEIN / paramyxovirus / PIV5 / attachment protein / HN / receptor binding protein / ectodomain
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesSimian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5018 Å
AuthorsWelch, B.D. / Yuan, P. / Bose, S. / Kors, C.A. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin-Neuraminidase (HN) Ectodomain.
Authors: Welch, B.D. / Yuan, P. / Bose, S. / Kors, C.A. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
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_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_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_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)230,92524
Polymers226,1834
Non-polymers4,74320
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23900 Å2
ΔGint-146 kcal/mol
Surface area66940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.390, 194.390, 185.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 4 molecules DABC

#1: Protein
Hemagglutinin-neuraminidase


Mass: 56545.688 Da / Num. of mol.: 4 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Strain: W3 / Gene: HN / Plasmid: pBACgus-11 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04850, exo-alpha-sialidase

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Sugars , 3 types, 12 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-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.: 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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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, 696 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe chain names represent the author's most probable connectivity despite the chain breaks

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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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2011
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 118507 / Num. obs: 118507 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.596.10.522118681100
2.59-2.696.10.389117991100
2.69-2.826.20.28118321100
2.82-2.966.30.201117821100
2.96-3.156.40.138118391100
3.15-3.396.50.094118381100
3.39-3.736.50.071118671100
3.73-4.276.30.066118491100
4.27-5.386.30.057118781100
5.38-356.20.03711955199.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5018→34.364 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 0 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1972 1.7 %
Rwork0.1656 114108 -
obs0.1663 116080 97.81 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.914 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 183.92 Å2 / Biso mean: 50.8227 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.6002 Å20 Å2-0 Å2
2--2.6002 Å20 Å2
3----5.2003 Å2
Refinement stepCycle: LAST / Resolution: 2.5018→34.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15414 0 298 688 16400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116140
X-RAY DIFFRACTIONf_angle_d1.1821977
X-RAY DIFFRACTIONf_chiral_restr0.0782521
X-RAY DIFFRACTIONf_plane_restr0.0052792
X-RAY DIFFRACTIONf_dihedral_angle_d14.6925766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5018-2.56430.27831300.20897483761390
2.5643-2.63360.27211350.20817802793794
2.6336-2.71110.25791570.19767894805195
2.7111-2.79850.24751310.18968033816497
2.7985-2.89850.24051420.17898100824298
2.8985-3.01450.22821310.17298194832598
3.0145-3.15160.19941480.16648214836299
3.1516-3.31760.23891390.165483288467100
3.3176-3.52530.23041460.165383088454100
3.5253-3.79720.19571400.15782738413100
3.7972-4.17870.17031360.144583368472100
4.1787-4.7820.17341480.135183608508100
4.782-6.01950.18721340.156183548488100
6.0195-34.36680.19461550.188984298584100
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)
10.76690.7582-0.23732.15530.40390.7763-0.05280.46050.1628-1.0197-0.01990.6192-0.3225-0.51980.43820.9960.3831-0.40530.9352-0.24860.983516.5845190.3699-55.3235
21.1763-0.3730.05290.8902-0.08670.7870.13180.29010.2304-0.1343-0.0776-0.4869-0.13920.189-0.03110.11930.04160.03310.18990.02890.284365.6486227.3966-21.4826
30.99430.488-0.23780.3055-0.00230.26750.10730.5788-0.0955-0.67580.06610.42410.3301-0.1970.0721.09380.2582-0.4310.8044-0.08410.743927.1766201.0726-48.431
40.4266-0.12720.17240.3497-0.04140.4986-0.1043-0.7615-0.1290.53150.17750.2105-0.0355-0.3196-0.02850.27150.18020.03070.55730.2853-0.312734.9457227.396610.8374
56.59270.12062.66743.8385-0.30434.4426-0.26630.55030.0724-0.85270.04410.4864-0.6242-0.23190.07860.86120.0693-0.0380.66460.04230.807530.786190.9568-59.154
60.2622-0.0038-0.14680.32920.18851.1618-0.09270.3265-0.029-0.37770.09260.0784-0.0281-0.3756-0.02890.1956-0.14990.2250.41820.0761-0.422144.9307167.3617-52.4563
74.4523-0.05021.12961.3024-0.85365.6952-0.46490.2914-0.2696-1.06510.03680.6324-1.2467-1.33030.33660.93520.0606-0.26660.7904-0.08660.77523.1793182.7761-59.2565
81.35870.87620.00861.8714-0.66113.99520.1289-0.0271-0.1228-0.0076-0.0151-0.23420.2315-0.1087-0.12820.15-0.0294-0.0070.1003-0.01440.243960.4049167.9744-20.5191
90.8255-0.21841.09141.65420.33671.6883-0.11040.02880.0458-0.19530.0037-0.28980.07880.02580.13260.1301-0.01760.06220.192-0.0520.197860.4863180.8972-26.4803
101.3522-0.14550.35590.3925-0.07380.91360.0309-0.1549-0.07110.0227-0.0528-0.27120.00490.1829-0.00050.0626-0.0119-0.00710.1913-0.0430.397277.7292188.861-14.7065
111.65910.11390.51610.6893-0.06980.98940.0621-0.0672-0.1770.06110.0071-0.44750.19310.1343-0.04360.14950.0095-0.02910.182-00.381273.4508172.4617-15.544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 58:119)A58 - 119
2X-RAY DIFFRACTION2chain 'A' and (resseq 120:565)A120 - 565
3X-RAY DIFFRACTION3chain 'B' and (resseq 58:114)B58 - 114
4X-RAY DIFFRACTION4chain 'B' and (resseq 115:565)B115 - 565
5X-RAY DIFFRACTION5chain 'C' and (resseq 58:124)C58 - 124
6X-RAY DIFFRACTION6chain 'C' and (resseq 125:565)C125 - 565
7X-RAY DIFFRACTION7chain 'D' and (resseq 58:98)D58 - 98
8X-RAY DIFFRACTION8chain 'D' and (resseq 99:165)D99 - 165
9X-RAY DIFFRACTION9chain 'D' and (resseq 166:241)D166 - 241
10X-RAY DIFFRACTION10chain 'D' and (resseq 242:366)D242 - 366
11X-RAY DIFFRACTION11chain 'D' and (resseq 367:565)D367 - 565

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