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- PDB-8vf1: Crystal Structure of the Hendra Virus Attachment G glycoprotein (... -

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Basic information

Entry
Database: PDB / ID: 8vf1
TitleCrystal Structure of the Hendra Virus Attachment G glycoprotein (HeV-G)
ComponentsGlycoprotein G
KeywordsVIRAL PROTEIN / attachment protein
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHenipavirus hendraense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVe, T. / von Itzstein, M.S. / Winger, M. / Malde, A.K. / Holt, S. / McAtamney, S. / Hartley-Tassell, L. / Maggioni, A. / von Itzstein, M.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1047824 Australia
Australian Research Council (ARC)DP1094549 Australia
Australian Research Council (ARC)DE17010078 Australia
CitationJournal: To Be Published
Title: Nipah and Hendra Virus use an adjustable latch in Receptor Engagement
Authors: von Itzstein, M.S. / Winger, M. / Malde, A.K. / Holt, S. / McAtamney, S. / Hartley-Tassell, L. / Ve, T. / Maggioni, A. / von Itzstein, M.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein G
B: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4077
Polymers101,9212
Non-polymers2,4855
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.822, 80.155, 95.136
Angle α, β, γ (deg.)90.000, 106.483, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycoprotein G


Mass: 50960.621 Da / Num. of mol.: 2 / Fragment: residues 171-604
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus hendraense / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89343
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}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.: 3
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
Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30-36% PEG 4000, 0.2 M MgCl2, and 0.1 M Tris pH 8.0-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→45.61 Å / Num. obs: 16148 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.5 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.114 / Rrim(I) all: 0.211 / Net I/σ(I): 4.9
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.636 / Num. unique obs: 2554 / CC1/2: 0.634 / Rpim(I) all: 0.491 / Rrim(I) all: 0.808

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.61 Å / SU ML: 0.3674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 853 5.29 %
Rwork0.2149 15261 -
obs0.2176 16114 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.26 Å2
Refinement stepCycle: LAST / Resolution: 3→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 164 0 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326931
X-RAY DIFFRACTIONf_angle_d0.62759438
X-RAY DIFFRACTIONf_chiral_restr0.04831098
X-RAY DIFFRACTIONf_plane_restr0.00411190
X-RAY DIFFRACTIONf_dihedral_angle_d16.40992584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.32391360.25972517X-RAY DIFFRACTION97.72
3.19-3.430.28911290.25092498X-RAY DIFFRACTION97.99
3.43-3.780.30851550.23032500X-RAY DIFFRACTION98.48
3.78-4.330.27731360.20152571X-RAY DIFFRACTION99.85
4.33-5.450.22251530.18022549X-RAY DIFFRACTION99.93
5.45-45.610.24181440.2182626X-RAY DIFFRACTION99.71
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)
12.70668494881-0.9152526572431.109867611881.93084883757-0.5271061757765.679318693220.06059569788690.09857852719030.2312975980050.0783942753531-0.229030946963-0.423391381621-0.1227276355840.576961720010.1452647266990.264083752355-0.0606211593286-0.06820693717710.358841607873-0.03566125107580.3002724072288.231-9.377-15.569
26.5725664582-3.80310223178-1.863497627343.250073739642.19523684084.731319504480.2051132958010.6628578839080.102996966718-0.348711635182-0.385875640992-0.0170265954592-0.34982181162-0.3617514072070.1645175201380.307089595115-0.00761128164191-0.0169489863610.2745298103660.03439224900030.293180174201-10.722-8.603-19.081
39.40101659757-3.68673717757-5.013247659863.850388495891.469311282452.931744866460.2223913563961.33955303404-0.760472849094-0.608672848053-0.6663342400820.08693232306060.592052321871-1.026489677670.4937882151450.595053237394-0.03155996181670.03400611870420.624607278008-0.05085944069790.318257972604-8.749-20.038-26.921
41.632242118910.1902675916380.4350745558871.658243793090.2642216442051.823983212820.0340111375334-0.05842033827140.1736734513890.298409927648-0.06961410988570.0645289289603-0.106346812892-0.2958725567240.01500251661010.437242691280.02082213410710.03023124148850.368088857810.03046029561770.24727344329-7.644-8.2220.979
55.21005343591-0.06424079875830.694046669254.71733301128-1.826158619386.5688565857-0.143082821595-0.008198969762390.04661382556380.3155372811740.540545594885-0.484235175574-0.308566427548-0.391679707676-0.2866712332150.3162759276540.00564515008265-0.04825143076320.408202310037-0.03185873190930.22726967187712.167-10.692-7.798
63.90618084954-0.5358769692710.1645465820231.72617741855-0.4570884290644.663615453760.2329481843880.05847857539910.3230615617150.1351233502370.0382035150216-0.0347184407317-0.4085792860570.0291126649238-0.2190704838740.326646525863-0.0252052959550.07035356774020.359215998486-0.03823229491680.275544658461-41.276-9.629-36.503
72.3361009678-1.86788818591-0.3966432573721.840696624830.4895017114993.91029979206-0.369079881911-0.8022866044870.3571745270150.2143264633130.362731649392-0.181370167633-0.00739679949230.841704062240.077584173430.419134188131-0.0566563018803-0.05055472592830.7508543222850.05673570692250.308339922151-23.4-15.697-33.85
83.00431252731-0.407999601343-4.660347004745.36813239383-0.4175416199567.5305476446-0.0752297488331-1.128337123730.3236918997660.1546108828090.0754938803809-0.798565654205-0.2622547883361.321452866450.1925289931620.4698853321320.03971413424120.05490365119240.5513086911490.01713263977910.532792433675-28.929-26.326-27.168
93.0513722440.252913558536-0.8155161252233.02261902904-1.841550012255.21203236946-0.186326111951-0.06235112824920.0920150550256-0.480768376276-0.0631093545293-0.5286674885060.05853346994620.9784604936760.2282368240130.363151237678-0.00368661171853-0.01382944028310.544445279667-0.02493490779130.411376048015-16.397-13.988-52.576
104.22247859158-0.346721801722-0.2433858462622.94872404038-0.05722233436154.475771456520.1478601096460.117749324710.0190025843504-0.0895786057166-0.03794071906460.05899821233240.03853227738230.0754070969165-0.1165207046020.3069347679160.001621474822570.05091719858140.311914857131-0.01740754185860.212743385806-31.545-10.824-54.258
115.03919767151.326517662610.8546169914.660389871531.089636798432.66045355053-0.1306159119740.974851901730.456008953678-0.07668311303520.1385144262490.2180342804560.1443368332590.1092951019470.0761961857250.3371142097670.02687128537070.04631659391210.2932785578930.07184695073810.322226661579-44.859-8.307-43.73
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 186:271 )A186 - 271
2X-RAY DIFFRACTION2( CHAIN A AND RESID 272:320 )A272 - 320
3X-RAY DIFFRACTION3( CHAIN A AND RESID 321:341 )A321 - 341
4X-RAY DIFFRACTION4( CHAIN A AND RESID 342:560 )A342 - 560
5X-RAY DIFFRACTION5( CHAIN A AND RESID 561:603 )A561 - 603
6X-RAY DIFFRACTION6( CHAIN B AND RESID 185:271 )B185 - 271
7X-RAY DIFFRACTION7( CHAIN B AND RESID 272:320 )B272 - 320
8X-RAY DIFFRACTION8( CHAIN B AND RESID 321:341 )B321 - 341
9X-RAY DIFFRACTION9( CHAIN B AND RESID 342:417 )B342 - 417
10X-RAY DIFFRACTION10( CHAIN B AND RESID 418:560 )B418 - 560
11X-RAY DIFFRACTION11( CHAIN B AND RESID 561:602 )B561 - 602

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