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- PDB-6cnv: INFLUENZA B/BRISBANE HEMAGGLUTININ FAB CR9115 SD84H COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6cnv
TitleINFLUENZA B/BRISBANE HEMAGGLUTININ FAB CR9115 SD84H COMPLEX
Components
  • CR9114 Fab heavy chain
  • CR9114 Light chain
  • Envelope glycoprotein
  • Hemagglutinin
  • SD84h
KeywordsVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / influenza / Single domain antibody / hemagglutinin / humanization
Function / homology
Function and homology information


viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...viral budding from plasma membrane / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Fibritin C-terminal / Fibritin C-terminal region / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Envelope glycoprotein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza B virus
Human immunodeficiency virus 1
synthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsLuo, J. / Obmolova, G.
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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Envelope glycoprotein
C: SD84h
L: CR9114 Light chain
H: CR9114 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,35710
Polymers121,4385
Non-polymers1,9195
Water0
1
A: Hemagglutinin
B: Envelope glycoprotein
C: SD84h
L: CR9114 Light chain
H: CR9114 Fab heavy chain
hetero molecules

A: Hemagglutinin
B: Envelope glycoprotein
C: SD84h
L: CR9114 Light chain
H: CR9114 Fab heavy chain
hetero molecules

A: Hemagglutinin
B: Envelope glycoprotein
C: SD84h
L: CR9114 Light chain
H: CR9114 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,07130
Polymers364,31515
Non-polymers5,75615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Unit cell
Length a, b, c (Å)190.780, 190.780, 190.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 37699.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: U3RVK6
#2: Protein Envelope glycoprotein


Mass: 23910.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus, (gene. exp.) Human immunodeficiency virus 1
Production host: Homo sapiens (human)
References: UniProt: G4WYG8, UniProt: M1E1E4, UniProt: C0LT38*PLUS

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Antibody , 3 types, 3 molecules CLH

#3: Antibody SD84h


Mass: 12564.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#4: Antibody CR9114 Light chain


Mass: 22840.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody CR9114 Fab heavy chain


Mass: 24423.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 5 molecules

#6: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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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: 4.76 Å3/Da / Density % sol: 74.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate, pH 4.5, 5.5 M sodium formate, and 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→47.7 Å / Num. obs: 18421 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.996 / Net I/σ(I): 11.2
Reflection shellResolution: 4.1→4.21 Å / Redundancy: 10.6 % / Num. unique obs: 1349 / CC1/2: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→47.695 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.2762 919 4.99 %
Rwork0.2405 --
obs0.2422 18411 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.1→47.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7775 0 126 0 7901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048091
X-RAY DIFFRACTIONf_angle_d1.26411000
X-RAY DIFFRACTIONf_dihedral_angle_d13.0732896
X-RAY DIFFRACTIONf_chiral_restr0.0441266
X-RAY DIFFRACTIONf_plane_restr0.0061409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1002-4.31620.33221290.28222458X-RAY DIFFRACTION100
4.3162-4.58640.28961300.25272476X-RAY DIFFRACTION100
4.5864-4.94020.28281300.23132465X-RAY DIFFRACTION100
4.9402-5.43680.29351310.23962489X-RAY DIFFRACTION100
5.4368-6.2220.29571310.2352495X-RAY DIFFRACTION100
6.222-7.83340.27161320.25252510X-RAY DIFFRACTION100
7.8334-47.69820.24781360.22712599X-RAY DIFFRACTION100

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