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- PDB-8ja5: Crystal structure of Nipah Virus attachment (G) glycoprotein in c... -

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Basic information

Entry
Database: PDB / ID: 8ja5
TitleCrystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8
Components
  • (14F8 antibody light ...) x 2
  • 14F8 antibody heavy chain
  • Glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / Nipah virus / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Nipah henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsLi, Y.H. / Huang, X.Y. / Xu, J.J. / Chen, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200762 China
CitationJournal: To Be Published
Title: Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8
Authors: Li, Y.H. / Huang, X.Y. / Li, R.H. / Xu, J.J. / Chen, W.
History
DepositionMay 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 14F8 antibody heavy chain
L: 14F8 antibody light chain
A: Glycoprotein G
B: 14F8 antibody heavy chain
C: 14F8 antibody light chain
D: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,53814
Polymers193,1226
Non-polymers4,4168
Water1,08160
1
H: 14F8 antibody heavy chain
L: 14F8 antibody light chain
A: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7657
Polymers96,3143
Non-polymers2,4514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint7 kcal/mol
Surface area35140 Å2
MethodPISA
2
B: 14F8 antibody heavy chain
C: 14F8 antibody light chain
D: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7737
Polymers96,8083
Non-polymers1,9654
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-0 kcal/mol
Surface area34480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.957, 125.957, 317.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 3 types, 4 molecules HBLC

#1: Antibody 14F8 antibody heavy chain


Mass: 24967.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 14F8 antibody light chain


Mass: 23587.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody 14F8 antibody light chain


Mass: 24081.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 62 molecules AD

#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
#3: Protein Glycoprotein G


Mass: 47758.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah henipavirus / Production host: Homo sapiens (human) / References: UniProt: Q9IH62

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Sugars , 5 types, 8 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#9: 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.: 2 / Source method: obtained synthetically / 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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Details

Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.05M Ammonium sulfate, 10mM Barium chloride dihydrate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.79→36.83 Å / Num. obs: 63808 / % possible obs: 98.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 62.38 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.14
Reflection shellResolution: 2.79→2.89 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 63465

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VY5

6vy5


Resolution: 2.79→36.45 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 3143 4.95 %
Rwork0.2166 --
obs0.218 63451 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13130 0 293 60 13483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.548
X-RAY DIFFRACTIONf_dihedral_angle_d15.255034
X-RAY DIFFRACTIONf_chiral_restr0.1052179
X-RAY DIFFRACTIONf_plane_restr0.0112360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.840.41151520.35612536X-RAY DIFFRACTION94
2.84-2.880.38371290.33142668X-RAY DIFFRACTION98
2.88-2.930.32671190.32522691X-RAY DIFFRACTION98
2.93-2.990.33381340.30942670X-RAY DIFFRACTION98
2.99-3.050.31291500.29412651X-RAY DIFFRACTION98
3.05-3.110.32341440.27982702X-RAY DIFFRACTION99
3.11-3.170.30431330.27662681X-RAY DIFFRACTION99
3.17-3.250.3221360.27052734X-RAY DIFFRACTION99
3.25-3.330.30081260.27822723X-RAY DIFFRACTION99
3.33-3.420.24791460.26452740X-RAY DIFFRACTION99
3.42-3.520.25591380.2412721X-RAY DIFFRACTION100
3.52-3.630.26381520.22742739X-RAY DIFFRACTION100
3.63-3.760.24841490.21712712X-RAY DIFFRACTION100
3.76-3.910.25031490.20142760X-RAY DIFFRACTION100
3.91-4.090.24271490.19752754X-RAY DIFFRACTION100
4.09-4.310.19481320.17322771X-RAY DIFFRACTION100
4.31-4.580.21461510.16942771X-RAY DIFFRACTION100
4.58-4.930.18791700.15972766X-RAY DIFFRACTION100
4.93-5.420.1791380.17272824X-RAY DIFFRACTION100
5.42-6.210.24381350.20342825X-RAY DIFFRACTION100
6.21-7.80.22251550.20362873X-RAY DIFFRACTION100
7.81-36.450.22941560.20542996X-RAY DIFFRACTION99
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)
14.24771.6989-2.66287.2676-1.81672.40710.04880.2208-0.22530.25510.0210.11990.0415-0.0748-0.03580.30890.0359-0.07860.3848-0.01170.3063-1.0451-0.1495-56.048
21.92741.7265-0.31023.0638-0.01361.5945-0.0630.3973-0.0350.1373-0.02580.08270.3370.01010.12940.4350.04930.06040.48310.01330.2963-18.5288-7.7199-57.2009
35.3439-0.25082.59862.07460.59591.41340.03691.4050.1205-0.5952-0.21840.06290.24980.55170.33520.5977-0.08630.03450.83410.08930.4341-27.1917-14.8903-64.5147
47.76472.27257.333.21.60167.630.23290.50651.6090.2798-0.69830.70250.27590.07740.61660.4477-0.01880.1330.55620.06290.6658-22.612117.4788-49.8132
53.90792.6172-0.36477.35411.82270.8568-0.39390.56370.4657-0.66710.34950.6939-0.2123-0.104-0.02450.33730.014-0.03310.41680.12250.362-12.303517.8236-58.3671
67.4767-0.74843.77696.9481-2.57176.0759-0.33490.51291.33010.5937-0.20921.2475-1.1475-0.02320.54180.4851-0.06010.10090.52770.16210.8419-18.335823.8839-53.893
740.94371.42262.84950.44532.165-0.27340.4611.0165-0.1776-0.00620.9713-0.0195-0.36650.23390.3864-0.0616-0.02520.43210.09550.5915-22.607512.2905-55.5568
85.8322-2.84340.68499.27750.53411.85110.2701-0.2876-0.01980.983-0.36120.76070.1808-0.15090.19390.6208-0.30170.08470.7237-0.01520.4553-39.4009-13.482-55.4065
99.08163.0485-1.19084.5645-1.20032.5624-0.0444-1.682-0.39371.8674-0.48631.22390.5833-1.53490.21321.1425-0.41070.36451.4452-0.05450.7962-40.7074-14.4815-46.3716
106.75830.2990.36289.3139-6.83487.3022-0.02470.11860.3667-0.3805-0.7809-0.96680.5903-0.53971.0010.582-0.12260.04680.7584-0.02940.4456-34.5795-4.7385-57.0523
113.8059-0.44581.4210.90030.87282.56460.5892-0.5779-0.65061.0428-0.12821.55240.2182-0.3709-0.68710.8945-0.37780.23310.9226-0.17131.1548-46.842-16.021-51.9861
123.18010.91040.8232.4652-1.29143.8935-0.0269-0.3095-0.0260.2281-0.1268-0.50540.16190.19960.06830.4110.0442-0.01680.4229-0.05020.329323.211219.8011-54.5464
134.27210.7327-2.66843.7396-0.63872.0448-0.31080.2885-0.09710.09050.1587-0.2701-0.02240.35420.16150.30480.0263-0.01360.28670.02370.304524.790429.377-59.016
142.04672.12340.0887.66260.56541.7905-0.13880.3837-0.1998-0.66510.1443-0.3420.0250.1952-0.02320.31590.05870.00180.651-0.07130.321721.865312.0782-75.8045
152.92041.0367-0.62881.8160.15022.8984-0.09390.2851-0.4655-0.1770.0823-0.61750.26280.4719-0.00950.31720.11140.00310.5111-0.06620.515728.98064.8601-66.959
163.11861.6833-1.08253.4891.50722.1147-0.0353-0.6474-0.46310.67560.0346-0.58010.26020.3349-0.00980.51190.0876-0.1860.56390.1010.462124.2635.648-48.8566
171.588-0.0026-2.17073.928-0.42293.10060.0644-0.6532-0.06610.3936-0.0836-0.81270.25360.359-0.06340.43480.0553-0.09960.45460.02550.353427.308717.7593-50.8098
186.9467-2.3598-5.63656.09293.39448.0516-0.3664-0.6332-0.78451.14110.632-0.03221.64340.5729-0.13490.66750.0148-0.0530.41580.13970.4428-26.5843-9.6827-26.2336
192.3426-1.3075-1.53963.33070.61991.3944-0.114-0.3595-0.0633-0.02460.1594-0.30220.27170.1439-0.00570.51230.0243-0.02270.43370.04520.3027-23.2233-4.687-26.4588
203.2266-0.7261.83181.1594-1.67094.99250.0939-0.9959-0.66851.2110.1439-0.55971.0268-0.0526-0.20791.13430.2114-0.20850.93940.10960.6102-4.7448-16.6743-19.2948
217.5492-1.37942.73012.92990.12296.34980.0227-0.3071-0.0815-0.1390.0362-1.2363-0.05490.59-0.09610.40610.06570.090.54670.03210.8641-9.937716.5739-30.0088
227.7763-2.25230.63326.6671-0.19712.2631-0.188-0.7850.690.46630.2731-0.9398-0.0940.327-0.040.38820.001-0.03570.4493-0.13280.4045-19.092417.1498-22.6757
234.7163-1.8509-0.23412.7174-0.34871.1063-0.3419-0.9731.15430.52930.238-1.23690.11450.38580.09530.49930.1277-0.10850.6725-0.09450.7017-9.939910.7012-25.051
243.80310.91780.76044.26091.29344.07970.05120.1138-0.1790.18010.1363-0.87820.54520.6031-0.15090.66350.2546-0.18610.8434-0.03960.7676.4174-11.9098-29.063
251.98380.31320.42522.39770.41311.68920.02320.1669-0.9007-0.1990.3988-1.50160.47650.5354-0.52450.9660.4453-0.13241.0719-0.12771.358514.7411-15.7184-32.1708
260.9126-1.34-0.20322.45030.52553.29670.07020.2019-0.0422-0.2543-0.0990.44780.1673-0.2470.06990.3986-0.0249-0.00420.45210.12740.4483-55.914217.8659-26.8264
272.0064-1.60640.33774.0705-0.66761.1809-0.381-0.7078-0.42840.87610.39020.64140.2408-0.11920.00140.53330.07610.18570.68880.17860.5154-56.499810.5213-8.1487
283.5559-0.4724-0.063.8230.06951.9427-0.0641-0.0177-0.7637-0.15110.04841.1220.3581-0.3698-0.00530.4033-0.0937-0.03170.41620.05310.6858-60.3124.7707-25.8472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 82 )
2X-RAY DIFFRACTION2chain 'H' and (resid 83 through 148 )
3X-RAY DIFFRACTION3chain 'H' and (resid 149 through 216 )
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 25 )
5X-RAY DIFFRACTION5chain 'L' and (resid 26 through 66 )
6X-RAY DIFFRACTION6chain 'L' and (resid 67 through 80 )
7X-RAY DIFFRACTION7chain 'L' and (resid 81 through 118 )
8X-RAY DIFFRACTION8chain 'L' and (resid 119 through 155 )
9X-RAY DIFFRACTION9chain 'L' and (resid 156 through 168 )
10X-RAY DIFFRACTION10chain 'L' and (resid 169 through 187 )
11X-RAY DIFFRACTION11chain 'L' and (resid 188 through 214 )
12X-RAY DIFFRACTION12chain 'A' and (resid 186 through 243 )
13X-RAY DIFFRACTION13chain 'A' and (resid 244 through 271 )
14X-RAY DIFFRACTION14chain 'A' and (resid 272 through 406 )
15X-RAY DIFFRACTION15chain 'A' and (resid 407 through 526 )
16X-RAY DIFFRACTION16chain 'A' and (resid 527 through 560 )
17X-RAY DIFFRACTION17chain 'A' and (resid 561 through 602 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 17 )
19X-RAY DIFFRACTION19chain 'B' and (resid 18 through 148 )
20X-RAY DIFFRACTION20chain 'B' and (resid 149 through 216 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 25 )
22X-RAY DIFFRACTION22chain 'C' and (resid 26 through 80 )
23X-RAY DIFFRACTION23chain 'C' and (resid 81 through 118 )
24X-RAY DIFFRACTION24chain 'C' and (resid 119 through 187 )
25X-RAY DIFFRACTION25chain 'C' and (resid 188 through 211 )
26X-RAY DIFFRACTION26chain 'D' and (resid 186 through 243 )
27X-RAY DIFFRACTION27chain 'D' and (resid 244 through 430 )
28X-RAY DIFFRACTION28chain 'D' and (resid 431 through 602 )

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