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- PDB-3t1e: The structure of the Newcastle disease virus hemagglutinin-neuram... -

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Basic information

Entry
Database: PDB / ID: 3t1e
TitleThe structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain reveals a 4-helix bundle stalk
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE / Beta-Propeller / 4 helix bundle / Hemagglutinin / Neuraminidase / Membrane protein / Ectodomain
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / 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
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesNewcastle disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsYuan, P. / Swanson, K. / Leser, G.P. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the Newcastle disease virus hemagglutinin-neuraminidase (HN) ectodomain reveals a four-helix bundle stalk.
Authors: Yuan, P. / Swanson, K.A. / Leser, G.P. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references / Derived calculations
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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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
E: Hemagglutinin-neuraminidase
F: Hemagglutinin-neuraminidase


Theoretical massNumber of molelcules
Total (without water)234,8154
Polymers234,8154
Non-polymers00
Water00
1
A: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
E: Hemagglutinin-neuraminidase
F: Hemagglutinin-neuraminidase

A: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
E: Hemagglutinin-neuraminidase
F: Hemagglutinin-neuraminidase


Theoretical massNumber of molelcules
Total (without water)469,6308
Polymers469,6308
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13340 Å2
ΔGint-107 kcal/mol
Surface area71730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.292, 138.292, 167.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsALTHOUGH 4 CHAINS (A, B, E, AND F) ARE PRESENT IN THE PDB FILE, THEY DO NOT REPRESENT 4 INDEPENDENT COPIES OF THE ENTIRE PROTEIN. INSTEAD, CHAINS E AND F ARE N-TERMINAL SEGMENTS OF CHAINS A AND B. THE MOST LIKELY CONNECTIVITY IS CHAINS E-A AND CHAINS F-B.

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Components

#1: Protein
Hemagglutinin-neuraminidase


Mass: 58703.734 Da / Num. of mol.: 4 / Fragment: NDV HN ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Newcastle disease virus / Strain: Chicken/Australia-Victoria/32 / Gene: HN / Cell (production host): Hi5, SF plus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12554, exo-alpha-sialidase
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE RESIDUE AT THIS POSITION IS ALA ACCORDING TO THE CRYSTAL STRUCTURE.

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 4000, 200 mM Li2SO4, 100 mM N-(2-Acetamido) Iminodiacetic Acid (ADA), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.301→105.409 Å / Num. all: 25047 / Num. obs: 25027 / % possible obs: 99.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 23.8 % / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.301→48.894 Å / SU ML: 0.93 / σ(F): 1.34 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3104 1239 4.95 %
Rwork0.2483 --
obs0.2513 25011 99.89 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 125.742 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8725 Å20 Å2-0 Å2
2--5.8725 Å20 Å2
3----11.745 Å2
Refinement stepCycle: LAST / Resolution: 3.301→48.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6976 0 0 0 6976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057160
X-RAY DIFFRACTIONf_angle_d1.0019784
X-RAY DIFFRACTIONf_dihedral_angle_d13.8312394
X-RAY DIFFRACTIONf_chiral_restr0.0711103
X-RAY DIFFRACTIONf_plane_restr0.0051307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.301-3.43280.3681530.30842573X-RAY DIFFRACTION100
3.4328-3.5890.35761320.26182581X-RAY DIFFRACTION100
3.589-3.77810.29331450.24962589X-RAY DIFFRACTION100
3.7781-4.01470.31841250.23842618X-RAY DIFFRACTION100
4.0147-4.32450.33511280.2332626X-RAY DIFFRACTION100
4.3245-4.75940.26151300.21342648X-RAY DIFFRACTION100
4.7594-5.44730.2661410.22412637X-RAY DIFFRACTION100
5.4473-6.86010.36361440.26972674X-RAY DIFFRACTION100
6.8601-48.89890.30551410.26062826X-RAY DIFFRACTION99
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)
16.63860.9318-0.93239.3797-0.10552.5207-0.25770.18950.1829-1.7437-0.02151.12840.34580.55550.25570.933-0.1435-0.29180.9709-0.09860.628-28.0802-62.1591-6.7045
24.2208-1.50364.19269.2427-3.36354.79861.47311.1956-1.7814-0.7431-0.407-0.1241.47611.4095-1.15770.8620.1045-0.10231.084-0.32250.7374-14.0358-57.08925.2644
37.56541.7687-1.91369.37211.96433.4776-2.5386-1.0392.29620.5941-0.053-2.95480.62432.45510.41230.7988-0.4027-0.2420.5448-0.47880.9553-10.9324-54.81287.1119
43.99761.2029-1.53744.2673-1.19362.91130.1936-1.14190.03930.47230.0891-0.11780.25170.4832-0.24950.6207-0.0509-0.20540.8222-0.05510.5537-23.356-63.03818.6313
56.07123.0366-0.50673.51221.04143.5790.3399-2.28411.4023-0.5143-0.8029-0.2077-1.43140.24550.34231.2482-0.1675-0.02411.0251-0.27491.55665.9561-40.2226-0.9933
68.88062.00770.88599.26635.88057.4427-0.02151.0425-0.6781-0.31971.2745-0.98660.53612.0493-0.66170.748-0.0555-0.13120.9174-0.04090.5067-5.1833-51.0015-13.0105
74.66950.97562.51162.230.34122.17050.4533-1.11260.0334-0.3795-0.7457-0.43971.151-1.00530.85641.2345-0.39340.21281.105-0.131.2851-8.7478-52.721-14.8517
86.04921.4653-1.98872.553-1.98393.5043-0.10410.48610.539-1.13320.2962-0.14570.36470.4498-0.2181.3346-0.17580.05660.6639-0.01270.87613.527-44.7794-26.4112
96.67483.793-2.72073.7717-0.28354.05450.4201-0.7754-1.0630.83390.1835-0.52870.1624-0.4867-0.58461.11070.0039-0.35480.86860.47541.3164-46.4211-55.05934.3081
105.52023.2468-0.04896.32641.16084.0558-2.14920.1273-2.1309-2.7939-1.33630.79912.5760.93582.45912.04910.18010.27150.8954-0.14392.7525-65.9387-67.5989-7.7824
118.78596.5678-3.2058.9632-1.33575.81630.06522.119-1.17691.06540.8806-0.42710.09770.2377-0.77210.83950.1728-0.05820.6019-0.03591.3496-42.9252-49.9842-6.1088
123.53950.1299-3.30544.35490.93974.6896-0.4571-0.6114-0.58550.1660.3473-0.38481.5290.0333-0.04721.2089-0.0207-0.32590.45140.12350.7713-25.1929-75.67087.2756
132.8724-2.3963-0.30742.52520.6067.16540.36711.1228-0.1217-0.64950.1902-0.55280.52490.8066-0.68550.9528-0.1612-0.13250.4564-0.01910.8938-21.4702-65.8023-5.9953
141.57980.69832.85586.8056-4.78847.06960.13050.05470.1345-1.6824-0.1425-0.94070.10631.9752-0.15250.61930.0090.30931.6261-0.32121.165616.0964-48.1453-15.1763
151.79370.16712.46928.71971.04925.08710.7359-0.90651.1350.5515-0.91730.18631.797120.1192-0.0894-0.47110.03121.3076-0.61241.15915.7994-47.6632-1.7952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 123:165)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 166:191)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 192:212)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 213:414)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 123:165)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 166:191)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 192:212)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 213:414)
9X-RAY DIFFRACTION9CHAIN E
10X-RAY DIFFRACTION10CHAIN F AND (RESSEQ 79:85)
11X-RAY DIFFRACTION11CHAIN F AND (RESSEQ 86:115)
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 415:525)
13X-RAY DIFFRACTION13CHAIN A AND (RESSEQ 526:569)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 415:525)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 526:569)

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