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- PDB-6z06: Crystal structure of Puumala virus Gc in complex with Fab 4G2 -

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Basic information

Entry
Database: PDB / ID: 6z06
TitleCrystal structure of Puumala virus Gc in complex with Fab 4G2
Components
  • Envelope polyprotein
  • Fab 4G2 Heavy chain
  • Fab 4G2 Light chain
KeywordsVIRAL PROTEIN / viral glycoprotein / class II fusion glycoprotein / neutralizing antibody complex / hantavirus glycoprotein Gc / bank vole antibody
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesMyodes glareolus (Bank vole)
Puumala orthohantavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsRissanen, I.R. / Stass, R. / Krumm, S.A. / Seow, J. / Hulswit, R.J.G. / Paesen, G.C. / Hepojoki, J. / Vapalahti, O. / Lundkvist, A. / Reynard, O. ...Rissanen, I.R. / Stass, R. / Krumm, S.A. / Seow, J. / Hulswit, R.J.G. / Paesen, G.C. / Hepojoki, J. / Vapalahti, O. / Lundkvist, A. / Reynard, O. / Volchkov, V. / Doores, K.J. / Huiskonen, J.T. / Bowden, T.A.
Funding support United Kingdom, Finland, European Union, 9items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N002091/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K024426/1 United Kingdom
Academy of Finland309605 Finland
European Research Council (ERC)649053European Union
Wellcome Trust203141/Z/16Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Elife / Year: 2020
Title: Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein.
Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / ...Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / Katie J Doores / Juha T Huiskonen / Thomas A Bowden /
Abstract: The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. ...The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc) lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.
History
DepositionMay 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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
H: Fab 4G2 Heavy chain
L: Fab 4G2 Light chain
A: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2257
Polymers98,7283
Non-polymers4974
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The complex was observed in and purified by gel filtration prior to crystallization.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-23 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.213, 50.449, 124.446
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 4G2 Heavy chain


Mass: 25018.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myodes glareolus (Bank vole) / Plasmid: pHLsec / Cell line (production host): HEK293T CRL-1573 / Production host: Homo sapiens (human)
#2: Antibody Fab 4G2 Light chain


Mass: 23881.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myodes glareolus (Bank vole) / Plasmid: pHLsec / Cell line (production host): HEK293T CRL-1573 / Production host: Homo sapiens (human)
#3: Protein Envelope polyprotein / M polyprotein


Mass: 49827.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puumala orthohantavirus / Gene: gpc / Plasmid: pHLsec / Cell line (production host): HEK 293T cells / Production host: Homo sapiens (human) / References: UniProt: Q9WJ31
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#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.: 1
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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG6000, 1 M LiCl, 0.1 M MES pH 6, 6% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 3.5→92.633 Å / Num. obs: 14920 / % possible obs: 99.77 % / Redundancy: 9.6 % / Biso Wilson estimate: 65 Å2 / Rpim(I) all: 0.14 / Rrim(I) all: 0.437 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
3.5-3.5581.57020.5111.48993
9.47-92.6338.88.88180.0570.173100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J81

5j81


Resolution: 3.5→92.633 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 726 4.87 %
Rwork0.2173 14177 -
obs0.2196 14903 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.95 Å2 / Biso mean: 70 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 3.5→92.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 32 0 6496
Biso mean--58.16 --
Num. residues----847
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5001-3.77040.34991530.2842276099
3.7704-4.14980.28891390.24922810100
4.1498-4.75020.27251310.19362832100
4.7502-5.98470.22481480.1882831100
5.9847-92.60.23141550.20842944100
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)
16.57862.62260.14282.56470.14190.6787-0.3148-1.070.48230.06050.2513-0.1048-0.29650.20330.06280.63190.04320.09610.5605-0.17790.4813-3.190410.0916-17.7477
22.68840.318-3.06461.43361.44455.7528-0.06771.04890.0879-0.7360.5574-0.1076-0.40.0507-0.17940.8349-0.1930.13690.9877-0.23820.517521.05911.2717-37.3757
33.9707-0.888-0.91561.57161.33482.38340.01660.3133-1.3465-0.21840.5536-0.96330.38170.72220.11690.6556-0.06090.12570.4755-0.34260.768-7.1321-9.8297-31.0969
40.42480.41380.76741.38140.75231.6565-0.54441.0547-2.1339-0.22520.6075-1.12240.00140.6164-0.40470.7109-0.0650.13180.9441-0.57651.216924.3752-3.7178-35.8
50.7091-0.0134-0.75111.2408-0.34556.66830.13350.1592-0.0325-0.37970.0412-0.105-0.47270.0019-0.00490.4277-0.00270.03160.15070.03350.3611-30.2729-1.4747-34.3797
60.50520.18110.2380.2195-0.43858.34230.0020.0839-0.0381-0.3321-0.06980.01860.01140.1511-0.06870.60470.00450.03780.2076-0.01030.4513-30.0495-1.55-32.9438
71.4967-1.0267-0.40841.26090.5340.4371-0.0881-0.1004-0.24160.12270.01470.0643-0.12130.0347-0.02150.5379-0.09060.00440.0797-0.04580.3243-43.92794.55622.9185
81.9349-0.84550.34712.31490.07740.0893-0.5775-0.6128-0.91410.47430.14750.39330.596-0.2860.14510.6144-0.06050.14080.2554-0.00120.5595-56.6036-2.07014.1094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 0 through 123 )H0 - 123
2X-RAY DIFFRACTION2chain 'H' and (resid 124 through 216 )H124 - 216
3X-RAY DIFFRACTION3chain 'L' and (resid -1 through 90 )L-1 - 90
4X-RAY DIFFRACTION4chain 'L' and (resid 91 through 211 )L91 - 211
5X-RAY DIFFRACTION5chain 'A' and (resid 668 through 797 )A668 - 797
6X-RAY DIFFRACTION6chain 'A' and (resid 798 through 946 )A798 - 946
7X-RAY DIFFRACTION7chain 'A' and (resid 947 through 1043 )A947 - 1043
8X-RAY DIFFRACTION8chain 'A' and (resid 1044 through 1101 )A0

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