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- PDB-7bwu: Restructuring hemagglutinin-neuraminidase (HN) of Newcastle disea... -

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Basic information

Entry
Database: PDB / ID: 7bwu
TitleRestructuring hemagglutinin-neuraminidase (HN) of Newcastle disease virus produced from Oryza sativa
ComponentsHemagglutinin-neuraminidase
KeywordsVIRAL PROTEIN / hemagglutinin-neuraminidase / Plant-produced / Restructuring tetramer
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 / membrane => GO:0016020 / 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 / membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesAvian avulavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMa, F.S. / Zhang, G.P.
CitationJournal: To Be Published
Title: Restructuring a dimer antigen in transgenic rice system for high efficient B cell activation: Development of a super effective vaccine against Newcastle Disease Virus
Authors: Ma, F.S. / Zhang, E.Q. / Xu, Q.R. / Guo, J.Q. / Zhang, G.P.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _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
B: Hemagglutinin-neuraminidase
D: Hemagglutinin-neuraminidase
A: Hemagglutinin-neuraminidase
C: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,93416
Polymers232,5214
Non-polymers1,41412
Water20,3751131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Comparing crystal structure with the structure envelop obtained by SAXS, the results show that the structure obtained by SAXS can be well matched with the crystal structure of HN tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-33 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 142.070, 191.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hemagglutinin-neuraminidase /


Mass: 58130.156 Da / Num. of mol.: 4 / Mutation: M443T
Source method: isolated from a genetically manipulated source
Details: Authos linked two HN domains in the expression but the link is missing in the coordinate and they don't know which two molecules should be linked together.
Source: (gene. exp.) Avian avulavirus 1 / Gene: HN / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: I7EFR1
#2: 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 / N-Acetylglucosamine


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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→41.53 Å / Num. obs: 188493 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.118 / Net I/σ(I): 15
Reflection shellResolution: 1.87→1.93 Å / Num. unique obs: 18656 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data processing
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T1E

3t1e


Resolution: 1.87→39.863 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.1951 9289 4.93 %
Rwork0.1668 --
obs0.1682 188462 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.96 Å2 / Biso mean: 38.5067 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.87→39.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13727 0 84 1131 14942
Biso mean--57.55 44.39 -
Num. residues----1779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714176
X-RAY DIFFRACTIONf_angle_d0.91919305
X-RAY DIFFRACTIONf_chiral_restr0.0562181
X-RAY DIFFRACTIONf_plane_restr0.0062478
X-RAY DIFFRACTIONf_dihedral_angle_d4.1658417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.89130.32063000.27445914
1.8913-1.91350.30883070.25965958
1.9135-1.93680.30023010.24965872
1.9368-1.96140.28753330.24195863
1.9614-1.98720.27243250.23165947
1.9872-2.01440.26993050.21365891
2.0144-2.04320.24082890.20845930
2.0432-2.07370.25422810.2025951
2.0737-2.10610.22312920.19395951
2.1061-2.14060.22463190.19045930
2.1406-2.17750.22463110.18275923
2.1775-2.21710.23543100.18755937
2.2171-2.25970.21953170.17955933
2.2597-2.30580.21562960.17885901
2.3058-2.3560.21073160.17295956
2.356-2.41080.2143430.17725925
2.4108-2.47110.20722950.1765979
2.4711-2.53790.22353050.17455944
2.5379-2.61250.21583470.17595921
2.6125-2.69680.20983230.17075947
2.6968-2.79320.19373020.16566005
2.7932-2.9050.20173280.16615945
2.905-3.03720.20992900.16325964
3.0372-3.19720.21563020.15985993
3.1972-3.39740.17042910.15256047
3.3974-3.65960.15752970.14446055
3.6596-4.02760.152830.14246057
4.0276-4.60960.15073110.13246077
4.6096-5.80480.16623430.14246106
5.8048-100.18813270.18356351
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)
10.9968-0.0874-0.02232.10230.3951.50440.05770.2928-0.0191-0.49790.0335-0.099-0.25320.0538-0.02050.3515-0.00890.06010.37120.00510.2752-63.2754-28.2995-67.2989
20.96570.26180.09591.82780.3661.4022-0.02410.4072-0.182-0.55550.0776-0.2191-0.11130.139-0.04170.38450.01870.07480.4596-0.11980.3056-63.2626-44.9725-75.9106
30.75790.0897-0.0191.08140.35091.03530.01770.1243-0.3498-0.06260.0724-0.12980.12390.1161-0.05870.21230.0164-0.01080.2771-0.080.3987-66.8212-52.1562-56.8872
40.7640.4248-0.02821.1352-0.04220.70810.0501-0.0533-0.08440.2249-0.03130.06880.07-0.02-0.03050.2414-0.00040.020.2056-0.01950.2356-11.6088-67.0075-34.7416
51.4886-0.1289-0.33921.691-0.01740.98690.0537-0.14090.17790.21360.03720.1505-0.109-0.0838-0.07070.21490.00480.04860.2247-0.03050.2764-19.8925-58.6764-37.474
60.87450.0920.04980.70140.1581.24190.0263-0.3059-0.01260.3751-0.03530.09750.0288-0.03060.0110.4953-0.03210.06250.3632-0.00770.283-13.8428-60.2566-14.2682
71.05710.32180.09051.0304-0.43341.13050.0509-0.0525-0.09780.318-0.0646-0.26520.00870.16720.02830.26110.0047-0.02140.22-0.01440.2268-1.9073-64.9615-32.287
81.2178-0.3318-0.3141.03510.00450.88570.02480.13320.0593-0.02290.07290.2866-0.0308-0.2283-0.10640.19090.014-0.00760.28290.04730.3353-24.8893-48.1501-51.8378
91.2887-0.15630.47032.36820.51810.9774-0.01550.0171-0.0411-0.07940.02410.16550.0143-0.0451-0.09050.2117-0.0007-0.01430.23720.01630.2868-19.7676-58.2735-49.284
100.87210.0933-0.22371.7787-0.20460.98120.01670.40790.0853-0.55510.07190.25340.0979-0.178-0.08140.3678-0.0053-0.09070.43910.05820.2759-18.6391-51.6326-72.45
110.9663-0.02210.00120.7859-0.21481.03350.03780.10730.42360.01340.03550.1083-0.1581-0.1023-0.05630.22090.01670.01620.28220.0460.4135-18.7624-39.3353-54.2492
120.72860.31880.03661.1513-0.26660.79610.0403-0.01540.03570.2371-0.0037-0.0201-0.13910.0166-0.03530.2563-0.0023-0.02230.19810.01530.2443-73.1968-23.6382-34.6893
131.5113-0.43840.38091.56360.07250.93380.0517-0.1012-0.20890.24650.0352-0.06050.08070.0466-0.08750.233-0.0051-0.05250.21690.0140.2628-64.716-32.1016-36.6886
140.8084-0.01930.11060.7578-0.20830.86620.0745-0.1076-0.24630.2899-0.1155-0.26210.03980.13040.04320.4315-0.018-0.14610.30760.02150.374-59.6728-35.9268-20.711
150.84940.01510.10331.1532-0.11671.26040.1585-0.2990.07010.5691-0.1005-0.0553-0.0341-0.0414-0.03070.5823-0.0755-0.02750.3310.00020.2429-73.9798-27.2737-10.4533
161.14450.3935-0.05230.76010.10691.14580.0881-0.1110.05260.3882-0.0350.2147-0.0477-0.1796-0.03810.28580.00390.0430.20580.00230.2171-83.864-27.062-29.0687
171.1090.00590.19130.92180.11820.7910.03990.104-0.179-0.01290.0412-0.28430.07470.2034-0.06630.20480.0245-0.00960.2896-0.03640.3833-59.6367-43.6764-50.7669
181.136-0.0215-0.3971.8776-0.17951.3150.03980.145-0.04280.0133-0.0064-0.1407-0.05620.049-0.09250.18520.00830.00310.2249-0.01810.2934-63.9768-32.7515-48.218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 230 through 320 )C230 - 320
2X-RAY DIFFRACTION2chain 'C' and (resid 321 through 444 )C321 - 444
3X-RAY DIFFRACTION3chain 'C' and (resid 445 through 569 )C445 - 569
4X-RAY DIFFRACTION4chain 'B' and (resid 126 through 192 )B126 - 192
5X-RAY DIFFRACTION5chain 'B' and (resid 193 through 229 )B193 - 229
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 477 )B230 - 477
7X-RAY DIFFRACTION7chain 'B' and (resid 478 through 569 )B478 - 569
8X-RAY DIFFRACTION8chain 'D' and (resid 122 through 192 )D122 - 192
9X-RAY DIFFRACTION9chain 'D' and (resid 193 through 229 )D193 - 229
10X-RAY DIFFRACTION10chain 'D' and (resid 230 through 477 )D230 - 477
11X-RAY DIFFRACTION11chain 'D' and (resid 478 through 568 )D478 - 568
12X-RAY DIFFRACTION12chain 'A' and (resid 126 through 192 )A126 - 192
13X-RAY DIFFRACTION13chain 'A' and (resid 193 through 229 )A193 - 229
14X-RAY DIFFRACTION14chain 'A' and (resid 230 through 285 )A230 - 285
15X-RAY DIFFRACTION15chain 'A' and (resid 286 through 444 )A286 - 444
16X-RAY DIFFRACTION16chain 'A' and (resid 445 through 568 )A445 - 568
17X-RAY DIFFRACTION17chain 'C' and (resid 125 through 192 )C125 - 192
18X-RAY DIFFRACTION18chain 'C' and (resid 193 through 229 )C193 - 229

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