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- PDB-7kyl: Powassan virus Envelope protein DIII in complex with neutralizing... -

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Basic information

Entry
Database: PDB / ID: 7kyl
TitlePowassan virus Envelope protein DIII in complex with neutralizing Fab POWV-80
Components
  • Envelope protein domain III
  • POWV-80 Fab heavy chain
  • POWV-80 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / Tick-borne flavivirus / domain III / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral capsid / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region
Similarity search - Function
Flavivirus capsid protein C / Flavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 ...Flavivirus capsid protein C / Flavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesPowassan virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsErrico, J.M. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: J.Exp.Med. / Year: 2021
Title: Broadly neutralizing monoclonal antibodies protect against multiple tick-borne flaviviruses.
Authors: VanBlargan, L.A. / Errico, J.M. / Kafai, N.M. / Burgomaster, K.E. / Jethva, P.N. / Broeckel, R.M. / Meade-White, K. / Nelson, C.A. / Himansu, S. / Wang, D. / Handley, S.A. / Gross, M.L. / ...Authors: VanBlargan, L.A. / Errico, J.M. / Kafai, N.M. / Burgomaster, K.E. / Jethva, P.N. / Broeckel, R.M. / Meade-White, K. / Nelson, C.A. / Himansu, S. / Wang, D. / Handley, S.A. / Gross, M.L. / Best, S.M. / Pierson, T.C. / Fremont, D.H. / Diamond, M.S.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: POWV-80 Fab heavy chain
L: POWV-80 Fab light chain
E: Envelope protein domain III
X: POWV-80 Fab heavy chain
Y: POWV-80 Fab light chain
Z: Envelope protein domain III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8778
Polymers118,8196
Non-polymers582
Water19,6001088
1
H: POWV-80 Fab heavy chain
L: POWV-80 Fab light chain
E: Envelope protein domain III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4324
Polymers59,4093
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: POWV-80 Fab heavy chain
Y: POWV-80 Fab light chain
Z: Envelope protein domain III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4454
Polymers59,4093
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.154, 62.557, 141.546
Angle α, β, γ (deg.)90.000, 97.970, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules EZ

#3: Protein Envelope protein domain III


Mass: 11315.041 Da / Num. of mol.: 2 / Fragment: Domain III of E protein, UNP residues 576-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Powassan virus / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q91LY1

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Antibody , 2 types, 4 molecules HXLY

#1: Antibody POWV-80 Fab heavy chain


Mass: 24806.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody POWV-80 Fab light chain


Mass: 23287.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 1090 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.95 %
Description: Flat triangles or squares - dataset collected on a square
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.16M ammonium sulfate, 0.08M sodium acetate, 20% w/v glycerol, 16% w/v PEG 4000
Temp details: 20c

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Vapor phase liquid N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→46.73 Å / Num. obs: 93018 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.046 / Rrim(I) all: 0.125 / Net I/σ(I): 10.9 / Num. measured all: 666279 / Scaling rejects: 652
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.532 / Num. measured all: 45594 / Num. unique obs: 6840 / CC1/2: 0.888 / Rpim(I) all: 0.222 / Rrim(I) all: 0.577 / Net I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
Blu-Icedata collection
XDSdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVB, 3UO1

1svb

3uo1


Resolution: 2→46.67 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1082 1.16 %
Rwork0.19 91892 -
obs0.191 92974 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.5 Å2 / Biso mean: 33.89 Å2 / Biso min: 15.73 Å2
Refinement stepCycle: final / Resolution: 2→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8202 0 2 1088 9292
Biso mean--50.38 40.68 -
Num. residues----1068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.090.27331370.24481141711554
2.09-2.20.28291320.2291141511547
2.2-2.340.26011350.22491142511560
2.34-2.520.29151340.22781145811592
2.52-2.770.28261360.22451141511551
2.77-3.170.2271350.20281151711652
3.17-40.19391350.16461152711662
4-46.670.1731380.15181171811856
Refinement TLS params.Method: refined / Origin x: 16.5333 Å / Origin y: 10.9902 Å / Origin z: -30.6259 Å
111213212223313233
T0.1125 Å2-0.0018 Å20.0271 Å2-0.2075 Å20.0276 Å2--0.2748 Å2
L0.283 °20.1422 °20.0102 °2-0.5817 °20.0473 °2--0.0943 °2
S-0.0148 Å °0.0102 Å °0.0284 Å °0.0038 Å °0.0331 Å °0.033 Å °0.0024 Å °0.0043 Å °-0.0176 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLH3 - 230
2X-RAY DIFFRACTION1ALLL1 - 213
3X-RAY DIFFRACTION1ALLE304 - 396
4X-RAY DIFFRACTION1ALLX3 - 230
5X-RAY DIFFRACTION1ALLY1 - 213
6X-RAY DIFFRACTION1ALLZ304 - 396
7X-RAY DIFFRACTION1ALLH301
8X-RAY DIFFRACTION1ALLY301
9X-RAY DIFFRACTION1ALLH401 - 611
10X-RAY DIFFRACTION1ALLX301 - 544
11X-RAY DIFFRACTION1ALLL301 - 573
12X-RAY DIFFRACTION1ALLE401 - 467
13X-RAY DIFFRACTION1ALLZ401 - 464
14X-RAY DIFFRACTION1ALLY401 - 629

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