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- PDB-3tsi: Structure of the parainfluenza virus 5 (PIV5) hemagglutinin-neura... -

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Basic information

Entry
Database: PDB / ID: 3tsi
TitleStructure of the parainfluenza virus 5 (PIV5) hemagglutinin-neuraminidase (HN) stalk domain
ComponentsHemagglutinin-neuraminidase
KeywordsVIRAL PROTEIN / four-helix bundle / four stranded coiled coil / 11-mer hydrophobic repeat / receptor binding protein / ectodomain
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesSimian virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.651 Å
AuthorsBose, S. / Welch, B.D. / Kors, C.A. / Yuan, P. / Jardetzky, T.S. / Lamb, R.A.
CitationJournal: J.Virol. / Year: 2011
Title: Structure and mutagenesis of the parainfluenza virus 5 hemagglutinin-neuraminidase stalk domain reveals a four-helix bundle and the role of the stalk in fusion promotion.
Authors: Bose, S. / Welch, B.D. / Kors, C.A. / Yuan, P. / Jardetzky, T.S. / Lamb, R.A.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Oct 21, 2015Group: Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Hemagglutinin-neuraminidase
D: Hemagglutinin-neuraminidase


Theoretical massNumber of molelcules
Total (without water)27,3954
Polymers27,3954
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-90 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.276, 101.276, 85.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Hemagglutinin-neuraminidase


Mass: 6848.696 Da / Num. of mol.: 4 / Fragment: stalk domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 5 / Strain: W3 / Gene: HN / Plasmid: pBACgus-3 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P04850, exo-alpha-sialidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 4.63 Å3/Da / Density % sol: 73.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4.5% Tascimate, 0.09 M HEPES, 9% PEG MME 5000, pH 7.0, 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: 0.97959
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 25, 2011
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 15107 / Num. obs: 14956 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.057 / Χ2: 1.008 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.75.60.3827271.0251100
2.7-2.745.60.3217551.0851100
2.74-2.85.60.277171.0251100
2.8-2.855.60.2127661.0071100
2.85-2.925.60.1917411.0421100
2.92-2.985.60.157321.0051100
2.98-3.065.60.1257761.011100
3.06-3.145.60.1127240.9761100
3.14-3.235.60.1017641.0111100
3.23-3.345.60.0857231.0111100
3.34-3.465.60.0797570.9541100
3.46-3.65.50.0747571.0141100
3.6-3.765.40.0697541.1091100
3.76-3.965.40.0617460.9961100
3.96-4.25.40.0537630.878199.9
4.2-4.535.30.0467650.955199.9
4.53-4.985.20.0447540.9199.7
4.98-5.75.20.0457701.101199.7
5.7-7.165.20.0417781.0211100
7.16-304.50.0386871.057182.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.65 Å29.24 Å
Translation2.65 Å29.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3T1E

3t1e


Resolution: 2.651→29.236 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.34 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 757 5.07 %Random
Rwork0.2019 ---
obs0.2037 14930 98.97 %-
all-15085 --
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.835 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 199.98 Å2 / Biso mean: 81.4618 Å2 / Biso min: 33.23 Å2
Baniso -1Baniso -2Baniso -3
1-7.1246 Å2-0 Å2-0 Å2
2--7.1246 Å20 Å2
3----14.2491 Å2
Refinement stepCycle: LAST / Resolution: 2.651→29.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 0 11 1477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061468
X-RAY DIFFRACTIONf_angle_d1.0882006
X-RAY DIFFRACTIONf_chiral_restr0.067281
X-RAY DIFFRACTIONf_plane_restr0.005247
X-RAY DIFFRACTIONf_dihedral_angle_d14.913528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.651-2.85520.30641280.286828332961100
2.8552-3.14230.26461640.214528072971100
3.1423-3.59620.23261680.21228282996100
3.5962-4.52820.23031670.166228573024100
4.5282-29.23760.231300.20972848297895
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)
14.98652.08441.96546.151.72946.5658-0.88760.60870.1509-2.44470.82981.5979-1.72380.48860.02210.41840.1139-0.05670.3220.07780.400233.206721.0548.8929
21.0847-0.5875-1.45647.91463.75.1982-0.23480.2593-0.0198-0.91520.9287-0.4406-0.54110.7464-0.72460.3956-0.0130.00290.38460.05360.399941.896316.22568.289
3-0.4644-0.580.72075.80022.7593.0755-0.0097-0.32840.191-0.0757-0.49582.07110.0584-0.58360.52960.33780.045-0.01680.5813-0.00910.702230.185216.22817.1333
41.673-0.06520.25273.5855-1.33982.6853-0.15590.1191-0.14961.03630.605-0.01711.39740.2418-0.31610.2941-0.05590.03460.32630.05020.389439.43527.016814.1793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA0
2X-RAY DIFFRACTION2CHAIN BB0
3X-RAY DIFFRACTION3CHAIN CC0
4X-RAY DIFFRACTION4CHAIN DD0

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