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- PDB-6fys: Structure of single domain antibody SD83 -

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Basic information

Entry
Database: PDB / ID: 6fys
TitleStructure of single domain antibody SD83
ComponentsSingle domain antibody SD83
KeywordsVIRAL PROTEIN / Influenza / single domain antibody / hemagglutinin
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaursen, N.S. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R56 AI117675 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R56 AI127371 United States
CitationJournal: Science / Year: 2018
Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson /
Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Single domain antibody SD83
A: Single domain antibody SD83
B: Single domain antibody SD83
D: Single domain antibody SD83
E: Single domain antibody SD83
F: Single domain antibody SD83
G: Single domain antibody SD83
H: Single domain antibody SD83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,00813
Polymers110,6988
Non-polymers3105
Water3,675204
1
C: Single domain antibody SD83


Theoretical massNumber of molelcules
Total (without water)13,8371
Polymers13,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Single domain antibody SD83


Theoretical massNumber of molelcules
Total (without water)13,8371
Polymers13,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Single domain antibody SD83


Theoretical massNumber of molelcules
Total (without water)13,8371
Polymers13,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Single domain antibody SD83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8992
Polymers13,8371
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Single domain antibody SD83


Theoretical massNumber of molelcules
Total (without water)13,8371
Polymers13,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Single domain antibody SD83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8992
Polymers13,8371
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Single domain antibody SD83


Theoretical massNumber of molelcules
Total (without water)13,8371
Polymers13,8371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Single domain antibody SD83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0234
Polymers13,8371
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.960, 85.700, 103.780
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Single domain antibody SD83


Mass: 13837.263 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M potassium formate, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 74300 / % possible obs: 98 % / Redundancy: 12.5 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rsym value: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.6 % / Num. unique obs: 7351 / CC1/2: 0.89 / Rpim(I) all: 0.33 / Rsym value: 0.63 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.446 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1999 2.69 %
Rwork0.201 --
obs0.2018 74233 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7583 0 20 204 7807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077814
X-RAY DIFFRACTIONf_angle_d0.87810609
X-RAY DIFFRACTIONf_dihedral_angle_d13.8844520
X-RAY DIFFRACTIONf_chiral_restr0.051169
X-RAY DIFFRACTIONf_plane_restr0.0051354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33471350.27545125X-RAY DIFFRACTION99
2.05-2.10540.33081500.28045079X-RAY DIFFRACTION97
2.1054-2.16740.31831440.25765139X-RAY DIFFRACTION99
2.1674-2.23730.31961260.24625172X-RAY DIFFRACTION98
2.2373-2.31730.30241430.24985093X-RAY DIFFRACTION97
2.3173-2.410.29531460.23615053X-RAY DIFFRACTION97
2.41-2.51970.3011360.22235207X-RAY DIFFRACTION99
2.5197-2.65250.26371480.22315224X-RAY DIFFRACTION99
2.6525-2.81860.29241440.22195184X-RAY DIFFRACTION99
2.8186-3.03620.29831480.22645171X-RAY DIFFRACTION98
3.0362-3.34150.26261410.20765152X-RAY DIFFRACTION98
3.3415-3.82470.19911440.18945108X-RAY DIFFRACTION97
3.8247-4.81710.16711410.15655252X-RAY DIFFRACTION99
4.8171-37.45250.17741530.1795275X-RAY DIFFRACTION98

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