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- PDB-7qqb: Crystal structure of the envelope glycoprotein complex of Puumala... -

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Basic information

Entry
Database: PDB / ID: 7qqb
TitleCrystal structure of the envelope glycoprotein complex of Puumala virus in complex with the scFv fragment of the broadly neutralizing human antibody ADI-42898
Components
  • Envelope polyprotein
  • Single Chain Variable Fragment (scFv) of ADI-42898
KeywordsVIRAL PROTEIN / hantavirus / neutralizing antibodies / fusion proteins / bunyavirus
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 / virion membrane / cell surface / signal transduction ...: / 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 / virion membrane / cell surface / signal transduction / metal 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
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesPuumala orthohantavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSerris, A. / Rey, F.A. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0011 France
CitationJournal: Sci Transl Med / Year: 2023
Title: Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody.
Authors: Mittler, E. / Serris, A. / Esterman, E.S. / Florez, C. / Polanco, L.C. / O'Brien, C.M. / Slough, M.M. / Tynell, J. / Groning, R. / Sun, Y. / Abelson, D.M. / Wec, A.Z. / Haslwanter, D. / ...Authors: Mittler, E. / Serris, A. / Esterman, E.S. / Florez, C. / Polanco, L.C. / O'Brien, C.M. / Slough, M.M. / Tynell, J. / Groning, R. / Sun, Y. / Abelson, D.M. / Wec, A.Z. / Haslwanter, D. / Keller, M. / Ye, C. / Bakken, R.R. / Jangra, R.K. / Dye, J.M. / Ahlm, C. / Rappazzo, C.G. / Ulrich, R.G. / Zeitlin, L. / Geoghegan, J.C. / Bradfute, S.B. / Sidoli, S. / Forsell, M.N.E. / Strandin, T. / Rey, F.A. / Herbert, A.S. / Walker, L.M. / Chandran, K. / Guardado-Calvo, P.
History
DepositionJan 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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: Envelope polyprotein
B: Envelope polyprotein
H: Single Chain Variable Fragment (scFv) of ADI-42898
L: Single Chain Variable Fragment (scFv) of ADI-42898
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,4778
Polymers254,4634
Non-polymers2,0144
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.876, 109.304, 149.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Antibody , 2 types, 4 molecules ABHL

#1: Protein Envelope polyprotein / M polyprotein


Mass: 95672.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puumala orthohantavirus / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0B4U5I0, UniProt: A0A6M3W7M6
#2: Antibody Single Chain Variable Fragment (scFv) of ADI-42898


Mass: 31558.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly)

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Sugars , 2 types, 3 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 2
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

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Non-polymers , 2 types, 27 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25%(w/v) PEG 1000, 0.1M Hepes 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→39.89 Å / Num. obs: 43057 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.037 / Rrim(I) all: 0.126 / Net I/σ(I): 14.2 / Num. measured all: 495751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.711.92.9125316844570.5030.8793.0430.9100
9.73-39.899.70.02989579250.9990.010.0357.498.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y5F

6y5f


Resolution: 2.6→39 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.249 --
Rwork0.212 --
obs-43057 100 %
Displacement parametersBiso max: 209.45 Å2 / Biso mean: 85.6355 Å2 / Biso min: 44.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 134 26 7834

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