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- PDB-6t3f: Crystal structure Nipah virus fusion glycoprotein in complex with... -

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Basic information

Entry
Database: PDB / ID: 6t3f
TitleCrystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment
Components
  • Fab66 heavy chain
  • Fab66 light chain
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN / Fusion Protein / Glycoprotein / Antibody / Fab
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesNipah virus
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAvanzato, V.A. / Pryce, R. / Walter, T.S. / Bowden, T.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/S007555/1 United Kingdom
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (United Kingdom)MR/N002091/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex.
Authors: Avanzato, V.A. / Oguntuyo, K.Y. / Escalera-Zamudio, M. / Gutierrez, B. / Golden, M. / Kosakovsky Pond, S.L. / Pryce, R. / Walter, T.S. / Seow, J. / Doores, K.J. / Pybus, O.G. / Munster, V.J. ...Authors: Avanzato, V.A. / Oguntuyo, K.Y. / Escalera-Zamudio, M. / Gutierrez, B. / Golden, M. / Kosakovsky Pond, S.L. / Pryce, R. / Walter, T.S. / Seow, J. / Doores, K.J. / Pybus, O.G. / Munster, V.J. / Lee, B. / Bowden, T.A.
History
DepositionOct 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0
L: Fab66 light chain
H: Fab66 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6888
Polymers102,3793
Non-polymers1,3095
Water00
1
F: Fusion glycoprotein F0
L: Fab66 light chain
H: Fab66 heavy chain
hetero molecules

F: Fusion glycoprotein F0
L: Fab66 light chain
H: Fab66 heavy chain
hetero molecules

F: Fusion glycoprotein F0
L: Fab66 light chain
H: Fab66 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,06424
Polymers307,1369
Non-polymers3,92815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area37240 Å2
ΔGint-130 kcal/mol
Surface area110080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.249, 149.249, 385.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 55418.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9IH63
#2: Antibody Fab66 light chain


Mass: 22968.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Fab66 heavy chain


Mass: 23991.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: 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.: 1
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
#5: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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: 6.05 Å3/Da / Density % sol: 79.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.094 M Tris pH 8.0 and 3.7 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→107.3 Å / Num. obs: 42722 / % possible obs: 99.6 % / Redundancy: 25.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.042 / Rrim(I) all: 0.215 / Net I/σ(I): 13.9
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 24.3 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2104 / CC1/2: 0.736 / Rpim(I) all: 0.456 / Rrim(I) all: 2.279 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EVM, 4JO1

5evm

4jo1


Resolution: 3.2→91.116 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2485 2113 4.95 %
Rwork0.2128 --
obs0.2145 42657 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 310.07 Å2 / Biso mean: 114.2593 Å2 / Biso min: 25.49 Å2
Refinement stepCycle: final / Resolution: 3.2→91.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 84 0 6644
Biso mean--142.87 --
Num. residues----870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.27410.37611390.3365264099
3.2741-3.3560.41931180.3215264599
3.356-3.44670.35141450.2768263299
3.4467-3.54820.26141440.2611263499
3.5482-3.66270.31011380.249264899
3.6627-3.79360.21831280.2319266199
3.7936-3.94550.26811410.2214266599
3.9455-4.12510.22451670.19372639100
4.1251-4.34250.22671520.18292670100
4.3425-4.61460.21281330.16752693100
4.6146-4.97090.18471480.16262726100
4.9709-5.47110.1921390.1872710100
5.4711-6.26260.24271510.21712758100
6.2626-7.88950.26141350.22952810100
7.8895-91.1160.26961350.2088301399
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)
10.19670.10880.16720.358-0.08910.71040.04790.0098-0.13510.06720.04970.0520.3476-0.25790.00050.2786-0.0324-0.04260.3017-0.01270.432864.2136-62.757414.7307
20.9779-0.0201-0.16470.9082-0.75551.49740.0188-0.06130.01470.1041-0.0042-0.0454-0.0341-0.057500.4356-0.0336-0.03320.40.04950.53367.4686-56.246726.6237
30.7223-0.1320.27420.26450.33290.74960.04390.25720.0112-0.24540.0069-0.0667-0.0073-0.0062-00.54180.04290.03550.5601-0.03240.587293.6977-48.6818-11.5185
40.03060.00960.05270.239-0.06090.0784-0.1904-0.5397-0.2157-0.1298-0.18760.0690.7944-0.68220.00011.0362-0.18990.09111.23850.10820.862851.0026-64.645263.6791
50.3922-0.01740.03660.322-0.06780.13750.2275-0.3937-0.2590.06670.0087-0.1931-0.1167-0.2708-0.00020.6517-0.0689-0.00061.04540.04080.586154.2622-52.662660.1456
60.60850.28610.17110.2324-0.02920.1280.0823-0.5553-0.02970.2267-0.1570.17550.45750.32690.00010.7753-0.04550.07081.20340.13790.785554.9316-57.963661.7993
70.04240.00440.0430.02980.01090.03510.6912-0.1004-0.3536-0.1883-0.06560.372-0.3656-0.08320.00060.8455-0.1555-0.06371.3699-0.06130.599349.1687-56.635446.4716
81.55810.5131-1.01151.078-0.25450.63460.0943-1.1254-0.26060.3059-0.49080.0410.0873-0.6935-0.31441.0078-0.19810.0652.2466-0.22270.733931.1629-54.366484.8677
90.46390.23320.24961.19450.30680.1673-0.1931-0.38910.04321.2270.5332-0.2690.6781-0.24390.00251.1483-0.30050.06742.3128-0.09270.784930.7698-59.184586.776
100.0366-0.07210.03040.1234-0.01660.04860.28430.34790.42770.55170.8145-0.11990.41830.3735-0.00021.6172-0.1596-0.03162.03040.0551.31622.8656-62.987183.4632
110.1283-0.63930.12113.5715-0.43530.49560.0368-0.240.246-0.022-0.1459-0.6411-0.5513-0.6981-0.36660.8151-0.10270.17792.4342-0.13040.370928.622-55.365483.8132
121.88230.6340.99772.14991.44971.13870.14671.0112-0.21580.2140.8758-0.67040.45060.91020.56311.225-0.14240.26212.24890.12640.475924.6122-59.760694.7047
130.5188-0.42350.11510.2833-0.17930.3005-0.2854-0.27020.041-0.12680.40540.04360.297-0.8552-0.00020.6773-0.02190.06841.26230.12860.787338.3165-46.713649.8432
140.0178-0.00810.02410.1418-0.10220.14620.4898-0.19680.4231-0.39150.71460.32150.5169-0.70340.02960.8037-0.01930.25541.1412-0.07981.112237.7708-36.835545.6051
150.0029-0.01730.02670.0401-0.09770.16540.5468-0.35370.87490.0205-0.07050.66770.5712-0.12990.01170.6456-0.04410.03231.60410.38060.831533.11-47.78952.8366
160.0743-0.0597-0.0070.0370.01520.03010.19030.13790.76320.39930.1621-0.5389-0.4975-0.4875-0.00020.5782-0.08770.02010.8613-0.0360.655749.3838-45.121253.4882
170.0130.03280.00940.03080.01070.0293-0.3184-0.01840.1898-0.513-0.275-0.028-0.4960.3559-0.00061.12570.15150.07192.0649-0.131.16321.4517-46.182462.7293
180.0192-0.04690.00080.03210.0206-0.00291.207-1.04910.3288-0.1352-0.01890.5497-0.34610.0880.00781.40370.1737-0.13112.9113-0.5641.450124.0299-44.247793.7102
190.06470.0272-0.0176-0.0289-0.0070.06480.33970.09570.0367-0.01980.3690.2516-1.1636-0.5930.00071.11720.19070.28062.1957-0.23681.169927.9473-42.193979.0425
200.00760.04160.03630.0594-0.01970.00690.26090.05470.40910.10270.0026-0.5462-0.12840.61380.00021.0906-0.12060.11352.18720.27421.071230.4-47.528877.672
210.0359-0.058-0.00720.06330.08320.07210.4780.22910.41660.0302-0.407-0.80290.9627-0.14910.00031.23740.2291-0.00432.2774-0.3071.165829.0736-41.663382.0199
220.0067-0.0178-0.0220.02150.02480.0209-0.09840.7335-0.00880.94810.16920.2840.2055-0.080.00171.84910.39120.31662.191-0.0861.935422.39-34.701675.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 24 through 153 )F24 - 153
2X-RAY DIFFRACTION2chain 'F' and (resid 154 through 282 )F154 - 282
3X-RAY DIFFRACTION3chain 'F' and (resid 283 through 477 )F283 - 477
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 25 )L1 - 25
5X-RAY DIFFRACTION5chain 'L' and (resid 26 through 61 )L26 - 61
6X-RAY DIFFRACTION6chain 'L' and (resid 62 through 93 )L62 - 93
7X-RAY DIFFRACTION7chain 'L' and (resid 94 through 101 )L94 - 101
8X-RAY DIFFRACTION8chain 'L' and (resid 102 through 129 )L102 - 129
9X-RAY DIFFRACTION9chain 'L' and (resid 130 through 149 )L130 - 149
10X-RAY DIFFRACTION10chain 'L' and (resid 150 through 162 )L150 - 162
11X-RAY DIFFRACTION11chain 'L' and (resid 163 through 187 )L163 - 187
12X-RAY DIFFRACTION12chain 'L' and (resid 188 through 211 )L188 - 211
13X-RAY DIFFRACTION13chain 'H' and (resid 10 through 66 )H10 - 66
14X-RAY DIFFRACTION14chain 'H' and (resid 67 through 77 )H67 - 77
15X-RAY DIFFRACTION15chain 'H' and (resid 78 through 94 )H78 - 94
16X-RAY DIFFRACTION16chain 'H' and (resid 95 through 106 )H95 - 106
17X-RAY DIFFRACTION17chain 'H' and (resid 107 through 119 )H107 - 119
18X-RAY DIFFRACTION18chain 'H' and (resid 120 through 134 )H120 - 134
19X-RAY DIFFRACTION19chain 'H' and (resid 135 through 157 )H135 - 157
20X-RAY DIFFRACTION20chain 'H' and (resid 158 through 175 )H158 - 175
21X-RAY DIFFRACTION21chain 'H' and (resid 176 through 197 )H176 - 197
22X-RAY DIFFRACTION22chain 'H' and (resid 198 through 208 )H198 - 208

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