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- PDB-6cnw: STRUCTURE OF HUMANIZED SINGLE DOMAIN ANTIBODY SD84 -

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Basic information

Entry
Database: PDB / ID: 6cnw
TitleSTRUCTURE OF HUMANIZED SINGLE DOMAIN ANTIBODY SD84
Componentshumanized antibody SD84h
KeywordsIMMUNE SYSTEM / single domain antibody / humanization / influenza / hemagglutinin
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological specieshybrid (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsLuo, J. / Obmolova, O.
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 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: humanized antibody SD84h
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1678
Polymers12,5651
Non-polymers6027
Water2,198122
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)54.570, 54.570, 35.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody humanized antibody SD84h


Mass: 12564.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) hybrid / Cell line (production host): HEK293Fexpi / Production host: Homo sapiens (human)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.4 M (NH4)2SO4, 0.1 M sodium acetate, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.92→26.27 Å / Num. obs: 63610 / % possible obs: 86.2 % / Redundancy: 5.76 % / CC1/2: 1 / Net I/σ(I): 20.39
Reflection shellResolution: 0.92→0.97 Å / Redundancy: 2.46 % / Mean I/σ(I) obs: 2.17 / Num. unique obs: 3146 / CC1/2: 0.78 / % possible all: 29.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.92→24.404 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.26
RfactorNum. reflection% reflection
Rfree0.1394 3179 5 %
Rwork0.1257 --
obs0.1263 63552 86.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.92→24.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 38 122 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006966
X-RAY DIFFRACTIONf_angle_d1.0091304
X-RAY DIFFRACTIONf_dihedral_angle_d22.263347
X-RAY DIFFRACTIONf_chiral_restr0.088138
X-RAY DIFFRACTIONf_plane_restr0.006166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9201-0.93380.1944270.2873502X-RAY DIFFRACTION17
0.9338-0.94840.2233470.2374891X-RAY DIFFRACTION30
0.9484-0.9640.2266670.20391271X-RAY DIFFRACTION42
0.964-0.98060.196880.17591672X-RAY DIFFRACTION56
0.9806-0.99840.15451100.15012088X-RAY DIFFRACTION70
0.9984-1.01760.15031450.12982763X-RAY DIFFRACTION91
1.0176-1.03840.11371570.11712982X-RAY DIFFRACTION100
1.0384-1.0610.12381600.10653023X-RAY DIFFRACTION100
1.061-1.08560.12671580.09983016X-RAY DIFFRACTION100
1.0856-1.11280.11661580.09363005X-RAY DIFFRACTION100
1.1128-1.14290.11461580.09192986X-RAY DIFFRACTION100
1.1429-1.17650.10521570.09362990X-RAY DIFFRACTION100
1.1765-1.21450.10831590.09683030X-RAY DIFFRACTION100
1.2145-1.25790.11171580.09743001X-RAY DIFFRACTION100
1.2579-1.30820.09721580.10323004X-RAY DIFFRACTION99
1.3082-1.36780.12571600.11223025X-RAY DIFFRACTION100
1.3678-1.43990.13631580.11382999X-RAY DIFFRACTION100
1.4399-1.53010.13511570.11322984X-RAY DIFFRACTION99
1.5301-1.64820.1411590.12153029X-RAY DIFFRACTION99
1.6482-1.8140.13381580.12942993X-RAY DIFFRACTION99
1.814-2.07640.13011570.12782997X-RAY DIFFRACTION99
2.0764-2.61560.14191600.13343026X-RAY DIFFRACTION99
2.6156-24.4130.17321630.14793096X-RAY DIFFRACTION99

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