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- PDB-4fqy: Crystal structure of broadly neutralizing antibody CR9114 bound t... -

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Basic information

Entry
Database: PDB / ID: 4fqy
TitleCrystal structure of broadly neutralizing antibody CR9114 bound to H3 influenza hemagglutinin
Components
  • Antibody CR9114 heavy chain
  • Antibody CR9114 light chain
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral fusion protein / immunoglobulin / virus attachment and entry / immune recognition / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.253 Å
AuthorsEkiert, D.C. / Dreyfus, C. / Wilson, I.A.
CitationJournal: Science / Year: 2012
Title: Highly conserved protective epitopes on influenza B viruses.
Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt ...Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen /
Abstract: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. ...Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR9114 heavy chain
L: Antibody CR9114 light chain


Theoretical massNumber of molelcules
Total (without water)101,9834
Polymers101,9834
Non-polymers00
Water0
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR9114 heavy chain
L: Antibody CR9114 light chain

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR9114 heavy chain
L: Antibody CR9114 light chain

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Antibody CR9114 heavy chain
L: Antibody CR9114 light chain


Theoretical massNumber of molelcules
Total (without water)305,94812
Polymers305,94812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Unit cell
Length a, b, c (Å)203.710, 203.710, 203.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Hemagglutinin HA1 / hemagglutinin receptor binding subunit HA1


Mass: 35506.949 Da / Num. of mol.: 1 / Fragment: UNP residues 27-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 / hemagglutinin membrane fusion subunit HA2


Mass: 20041.131 Da / Num. of mol.: 1 / Fragment: UNP residues 346-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q91MA7
#3: Antibody Antibody CR9114 heavy chain


Mass: 23594.311 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)
#4: Antibody 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) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human)
Sequence detailsTHE AUTHORS STATE THAT R468G IS A NATURAL VARIANT.

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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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 200 mM zinc acetate, 14% PEG1000, 100 mM sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 5.25→50 Å / Num. obs: 5386 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 20.2 % / Rsym value: 0.09 / Net I/σ(I): 27.3
Reflection shellResolution: 5.25→5.35 Å / Redundancy: 9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.88 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.253→48.015 Å / SU ML: 1.12 / σ(F): 1.35 / Phase error: 52.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.374 517 9.62 %RANDOM
Rwork0.3661 ---
obs0.3661 5374 99.7 %-
Solvent computationShrinkage radii: 1.4 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.253→48.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 0 0 6982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017337
X-RAY DIFFRACTIONf_angle_d1.2819988
X-RAY DIFFRACTIONf_dihedral_angle_d12.9792654
X-RAY DIFFRACTIONf_chiral_restr0.081107
X-RAY DIFFRACTIONf_plane_restr0.0061306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.253-5.78060.42191270.44061190X-RAY DIFFRACTION99
5.7806-6.61520.39961110.41991224X-RAY DIFFRACTION100
6.6152-8.32740.46521410.41551189X-RAY DIFFRACTION100
8.3274-48.01690.33331380.33381254X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39391.3459-1.13511.1583-0.14332.04540.3867-0.6228-0.74960.3207-2.0412-1.42510.7592-0.4605-5.0088-1.63692.38871.113-0.3544-0.54840.681358.578418.6184-16.3812
22.07571.3395-1.47634.22230.55281.88360.42940.00570.7322-1.4731.20092.6651.0624-0.37661.1511.02580.6007-0.56983.20360.66060.524937.075351.6226-47.916
31.0824-0.82190.24580.8336-0.1660.63920.57820.5289-0.3504-0.6739-0.78160.65060.2824-1.3319-0.3578-0.80330.1918-0.6342.4309-0.01340.616812.984734.4171-42.2231
40.22840.27730.23850.2821-0.0320.2496-0.7447-0.3196-0.52910.06080.92922.44391.0618-0.8137-0.0073.3367-0.27730.68272.81030.42162.4003-2.80716.3976-27.4995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain H and resid 1:117 or chain L and resid 2:111
4X-RAY DIFFRACTION4chain H and resid 119:213 or chain L and resid 113:208

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