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- PDB-4fzh: Structure of the Ulster Strain Newcastle Disease Virus Hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 4fzh
TitleStructure of the Ulster Strain Newcastle Disease Virus Hemagglutinin-Neuraminidase Reveals Auto-Inhibitory Interactions Associated with Low Virulence
ComponentsHemagglutinin-neuraminidase
KeywordsHYDROLASE
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 / virion 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: 3.5008 Å
AuthorsYuan, P. / Paterson, R.G. / Leser, G.P. / Lamb, R.A. / Jardetzky, T.S.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structure of the ulster strain newcastle disease virus hemagglutinin-neuraminidase reveals auto-inhibitory interactions associated with low virulence.
Authors: Yuan, P. / Paterson, R.G. / Leser, G.P. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Hemagglutinin-neuraminidase
D: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,37615
Polymers236,1304
Non-polymers3,24611
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7988
Polymers118,0652
Non-polymers1,7346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-12 kcal/mol
Surface area36660 Å2
MethodPISA
3
C: Hemagglutinin-neuraminidase
D: Hemagglutinin-neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5777
Polymers118,0652
Non-polymers1,5125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-15 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.606, 124.606, 284.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Hemagglutinin-neuraminidase


Mass: 59032.398 Da / Num. of mol.: 4 / Fragment: HEAD DOMAIN UNP Residues 124-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Newcastle disease virus / Strain: chicken/N. Ireland/Ulster/67 / Gene: HN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12558, exo-alpha-sialidase
#2: 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
#3: 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.: 7
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 17% PEG 8000, 200 mM MgCl2, 100 mM Tris, pH 7.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.5→46.913 Å / Num. obs: 33126

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHASERfor MRphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8T

1e8t


Resolution: 3.5008→46.913 Å / SU ML: 1.05 / σ(F): 1.34 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3042 1662 5.06 %
Rwork0.2361 --
obs0.2395 32817 99.13 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.582 Å2 / ksol: 0.268 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5008→46.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15032 0 210 0 15242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615659
X-RAY DIFFRACTIONf_angle_d1.0421291
X-RAY DIFFRACTIONf_dihedral_angle_d15.4015664
X-RAY DIFFRACTIONf_chiral_restr0.0712400
X-RAY DIFFRACTIONf_plane_restr0.0052735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5008-3.60370.43891210.34932585X-RAY DIFFRACTION100
3.6037-3.720.33561320.31172578X-RAY DIFFRACTION100
3.72-3.85290.35511380.30542568X-RAY DIFFRACTION100
3.8529-4.00710.3781580.28962569X-RAY DIFFRACTION100
4.0071-4.18940.36511400.27072564X-RAY DIFFRACTION100
4.1894-4.41010.31261410.23712593X-RAY DIFFRACTION100
4.4101-4.68620.25381400.20772580X-RAY DIFFRACTION100
4.6862-5.04760.24821280.18662596X-RAY DIFFRACTION99
5.0476-5.55480.26581470.2062601X-RAY DIFFRACTION100
5.5548-6.35690.36611440.24982639X-RAY DIFFRACTION100
6.3569-8.00260.28041370.21062629X-RAY DIFFRACTION99
8.0026-46.91760.27811360.2242653X-RAY DIFFRACTION94
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)
12.3151.2735-1.02372.5115-0.49221.9107-0.1606-0.62920.29610.42680.64040.5157-0.3167-0.9782-0.25480.4780.14620.21622.2035-0.4470.7659-31.072711.600215.2727
27.98560.156-6.58193.3591-0.80575.5644-1.3375-0.76720.3722-0.13430.71710.1602-0.28750.40060.13520.4810.0981-0.02651.9502-0.57391.056-25.009420.955110.9265
31.4861-0.26950.58075.5131-1.86451.0204-0.3038-0.97770.83120.6110.2018-1.6076-0.3924-0.10690.1560.67090.072-0.2231.5069-0.4241.0459-7.45216.622615.7058
43.0425-0.6117-0.35015.22580.27890.9357-0.1619-0.4651-0.23060.4297-0.0858-0.76220.11480.00080.20060.43420.12010.1031.6078-0.16340.5085-11.7224-2.853117.0556
56.2780.0945-1.38134.4336-1.42361.47940.0145-1.0656-0.65910.04810.43390.25250.0039-0.0321-0.28760.30290.00780.06241.2318-0.33620.5617-29.04860.89039.5564
61.78-1.25072.24692.49490.55775.6872-0.2824-0.4674-0.11260.45570.12720.98450.8192-1.16530.20160.444-0.07760.44951.5337-0.4060.8269-37.78585.00949.3495
71.99421.22261.68315.6441-3.55985.7304-0.14740.39290.7132-1.14530.38461.02721.5216-0.2436-0.15490.62950.1275-0.00291.2037-0.28751.1227-30.14042.3219-10.3838
84.25550.0693-0.2610.8263-1.46912.6193-0.1143-0.53390.93980.3256-0.261-0.3236-0.8918-0.54840.18430.77780.19440.12840.9949-0.64051.6857-29.786437.0701-0.6993
93.8111-0.5520.22281.5008-1.60412.8545-0.4458-0.19610.89050.29420.250.4291-0.2191-0.8190.20590.63260.1720.0581.1344-0.38951.6811-48.46640.0216-5.8794
104.01711.89830.09392.22670.03393.2854-0.39180.76480.8717-0.14180.21320.2348-0.04030.02020.22560.36780.14310.00520.8233-0.18551.2846-31.709436.5994-12.8091
114.17875.2279-3.59296.8838-2.98019.44540.8736-1.0908-0.3165-0.3236-1.41450.4902-0.63070.83890.36570.49920.03650.11021.0001-0.47251.2772-22.960134.6591-9.0915
127.75095.0339-0.69246.7195-2.88527.3003-0.0978-0.01450.2815-1.447-0.2147-1.5780.62990.27840.17140.59870.14870.01981.0741-0.00281.2159-30.255118.1357-20.2885
130.7092-0.4745-0.21351.6043-0.58544.1526-0.0034-0.99860.09881.27360.2431-0.2699-0.05010.13580.13162.34190.3453-1.41621.3745-0.05310.94241.612445.482444.3325
142.7836-0.6721.67651.78510.58271.58630.1607-0.2089-0.47911.18281.1248-0.32860.30460.7212-0.80942.10710.4349-0.87621.484-0.42741.42594.09140.808933.57
154.6091-2.7172-0.16127.15591.14220.30260.38830.0703-0.93410.82120.33280.07790.25730.3327-0.61611.88570.1275-0.62561.0445-0.11140.8938-10.722446.278223.5817
162.3151-1.5681-0.71974.58580.43830.2505-0.3447-0.23780.29221.26120.3871-0.44280.4681-0.6054-0.03331.79850.0755-0.3041.41210.12190.7107-15.576261.152934.3508
174.1176-1.47872.37281.56610.41395.4099-0.3385-1.24020.4022-0.15180.4597-0.23491.0251-0.9482-0.08392.34710.2936-0.76550.9811-0.06891.0062-6.227861.976843.5357
182.75720.54751.22441.1730.16252.4735-0.0497-1.1716-0.00980.60260.0699-0.5157-0.68920.0176-0.10372.29790.211-1.38271.2454-0.48241.35886.482853.734944.7501
195.7393-0.2383.73982.14882.74759.6983-0.3929-0.77990.18130.48230.93820.053-1.5312-0.5229-0.0912.80910.6682-0.8991.1678-0.25621.09818.080752.2750.1131
204.66970.0983-0.93830.5713-1.12382.28450.9701-0.73450.41651.47330.1463-1.40570.61191.2127-0.18831.56620.953-0.92590.9203-0.26742.089418.597865.295836.5536
210.14080.3842-0.39683.2925-0.15191.64790.60820.3683-0.698-0.6868-0.5841-0.82540.5970.4057-0.01262.3290.7327-1.13121.5718-0.39012.226220.166931.034325.5072
221.7451-0.5293-0.21260.33020.4740.96590.00490.1831-0.35740.39470.1982-0.77820.26320.8303-0.0291.92931.0606-1.44771.2576-0.32262.368535.608826.776236.8947
230.89960.382-0.17982.2355-1.41250.97460.17670.3313-0.31910.70610.3344-1.48650.29311.1311-0.491.53330.6344-0.67081.4813-0.49462.355730.536536.512922.0024
244.1816-5.4813-5.46317.16217.1527.14190.6681.71711.3078-1.2359-0.9404-0.7474-2.2522-2.66880.46451.74620.3417-0.58881.7629-0.10782.384322.16338.261817.3037
251.15820.7076-0.82683.19932.8314.57520.2182-0.2180.9745-1.12250.0176-1.4143-0.17470.0162-0.1851.57760.6562-0.56991.8864-0.36072.576930.601756.194325.6525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 124:192)
2X-RAY DIFFRACTION2chain 'A' and (resseq 193:229)
3X-RAY DIFFRACTION3chain 'A' and (resseq 230:300)
4X-RAY DIFFRACTION4chain 'A' and (resseq 301:459)
5X-RAY DIFFRACTION5chain 'A' and (resseq 460:555)
6X-RAY DIFFRACTION6chain 'A' and (resseq 556:571)
7X-RAY DIFFRACTION7chain 'A' and (resseq 578:615)
8X-RAY DIFFRACTION8chain 'B' and (resseq 124:192)
9X-RAY DIFFRACTION9chain 'B' and (resseq 193:459)
10X-RAY DIFFRACTION10chain 'B' and (resseq 460:555)
11X-RAY DIFFRACTION11chain 'B' and (resseq 556:571)
12X-RAY DIFFRACTION12chain 'B' and (resseq 578:615)
13X-RAY DIFFRACTION13chain 'C' and (resseq 124:192)
14X-RAY DIFFRACTION14chain 'C' and (resseq 193:229)
15X-RAY DIFFRACTION15chain 'C' and (resseq 230:300)
16X-RAY DIFFRACTION16chain 'C' and (resseq 301:423)
17X-RAY DIFFRACTION17chain 'C' and (resseq 424:506)
18X-RAY DIFFRACTION18chain 'C' and (resseq 507:555)
19X-RAY DIFFRACTION19chain 'C' and (resseq 556:571)
20X-RAY DIFFRACTION20chain 'C' and (resseq 578:615)
21X-RAY DIFFRACTION21chain 'D' and (resseq 124:192)
22X-RAY DIFFRACTION22chain 'D' and (resseq 193:459)
23X-RAY DIFFRACTION23chain 'D' and (resseq 460:555)
24X-RAY DIFFRACTION24chain 'D' and (resseq 556:571)
25X-RAY DIFFRACTION25chain 'D' and (resseq 578:615)

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