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- PDB-8xc4: Nipah virus attachment glycoprotein head domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 8xc4
TitleNipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5
Components
  • 1E5-VH
  • 1E5-VL
  • Glycoprotein
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / Henipavirus / Glycoprotein / Head domain / Antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase activity / 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
Biological speciesHenipavirus nipahense
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsFan, P.F. / Yu, C.M. / Chen, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204260 China
CitationJournal: Nat Commun / Year: 2024
Title: A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer.
Authors: Pengfei Fan / Mengmeng Sun / Xinghai Zhang / Huajun Zhang / Yujiao Liu / Yanfeng Yao / Ming Li / Ting Fang / Bingjie Sun / Zhengshan Chen / Xiangyang Chi / Li Chen / Cheng Peng / Zhen Chen / ...Authors: Pengfei Fan / Mengmeng Sun / Xinghai Zhang / Huajun Zhang / Yujiao Liu / Yanfeng Yao / Ming Li / Ting Fang / Bingjie Sun / Zhengshan Chen / Xiangyang Chi / Li Chen / Cheng Peng / Zhen Chen / Guanying Zhang / Yi Ren / Zixuan Liu / Yaohui Li / Jianmin Li / Entao Li / Wuxiang Guan / Shanshan Li / Rui Gong / Kaiming Zhang / Changming Yu / Sandra Chiu /
Abstract: The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) ...The Hendra and Nipah viruses (HNVs) are highly pathogenic pathogens without approved interventions for human use. In addition, the interaction pattern between the attachment (G) and fusion (F) glycoproteins required for virus entry remains unclear. Here, we isolate a panel of Macaca-derived G-specific antibodies that cross-neutralize HNVs via multiple mechanisms. The most potent antibody, 1E5, confers adequate protection against the Nipah virus challenge in female hamsters. Crystallography demonstrates that 1E5 has a highly similar binding pattern to the receptor. In cryo-electron microscopy studies, the tendency of 1E5 to bind to the upper or lower heads results in two distinct quaternary structures of G. Furthermore, we identify the extended outer loop β1S2-β1S3 of G and two pockets on the apical region of fusion (F) glycoprotein as the essential sites for G-F interactions. This work highlights promising drug candidates against HNVs and contributes deeper insights into the viruses.
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Oct 30, 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
A: Glycoprotein
B: Glycoprotein
C: 1E5-VH
D: 1E5-VL
E: 1E5-VH
F: 1E5-VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,35014
Polymers197,3336
Non-polymers5,0178
Water00
1
A: Glycoprotein
E: 1E5-VH
F: 1E5-VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1027
Polymers98,6673
Non-polymers2,4354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint10 kcal/mol
Surface area35760 Å2
MethodPISA
2
B: Glycoprotein
C: 1E5-VH
D: 1E5-VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2487
Polymers98,6673
Non-polymers2,5814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint14 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.422, 193.422, 198.111
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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Protein , 1 types, 2 molecules AB

#1: Protein Glycoprotein


Mass: 49310.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q4VCP5

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody 1E5-VH


Mass: 26120.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody 1E5-VL


Mass: 23235.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Sugars , 5 types, 8 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[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_c3-d1WURCSPDB2Glycan 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-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 2 / Source method: obtained synthetically / 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

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Details

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: 4.7 Å3/Da / Density % sol: 73.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 58116 / % possible obs: 97.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 9.57
Reflection shellResolution: 3.24→3.32 Å / Rmerge(I) obs: 0.189 / Num. unique obs: 58116

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VY5

6vy5


Resolution: 3.24→33.69 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 2001 3.49 %
Rwork0.218 --
obs0.219 57369 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.24→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13698 0 80 0 13778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514106
X-RAY DIFFRACTIONf_angle_d1.10919214
X-RAY DIFFRACTIONf_dihedral_angle_d15.5452081
X-RAY DIFFRACTIONf_chiral_restr0.0692235
X-RAY DIFFRACTIONf_plane_restr0.0072422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.320.33471350.31883671X-RAY DIFFRACTION90
3.32-3.410.32041380.29263945X-RAY DIFFRACTION97
3.41-3.510.28741410.26823950X-RAY DIFFRACTION97
3.51-3.630.33931390.25883942X-RAY DIFFRACTION97
3.63-3.760.27391430.25233944X-RAY DIFFRACTION97
3.76-3.910.27331440.21783923X-RAY DIFFRACTION96
3.91-4.080.22851480.21263935X-RAY DIFFRACTION96
4.08-4.30.21511360.19043984X-RAY DIFFRACTION97
4.3-4.570.21541500.17443976X-RAY DIFFRACTION97
4.57-4.920.21681440.17614002X-RAY DIFFRACTION97
4.92-5.410.20911460.18194012X-RAY DIFFRACTION97
5.41-6.190.20771450.21274038X-RAY DIFFRACTION97
6.19-7.780.28111440.23874022X-RAY DIFFRACTION95
7.79-33.690.24591480.22434024X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 59.5681 Å / Origin y: 27.1205 Å / Origin z: -24.4456 Å
111213212223313233
T0.4869 Å2-0.0099 Å2-0.0559 Å2-0.6858 Å20.0851 Å2--0.6876 Å2
L0.4991 °2-0.1181 °2-0.3018 °2-0.8147 °20.0043 °2--0.8358 °2
S-0.0339 Å °0.2088 Å °0.0047 Å °-0.0902 Å °0.1054 Å °0.2038 Å °0.1393 Å °-0.0975 Å °-0.046 Å °
Refinement TLS groupSelection details: all

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