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- PDB-4fqh: Crystal Structure of Fab CR9114 -

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Basic information

Entry
Database: PDB / ID: 4fqh
TitleCrystal Structure of Fab CR9114
Components
  • antibody CR9114 heavy chain
  • antibody CR9114 light chain
KeywordsIMMUNE SYSTEM / neutralizing antibodies / antibody affinity / antigens / epitope / glycosylation / hemagglutinin glycoproteins / immunoglobulin Fab fragment / influenza virus / influenza vaccines / membrane fusion
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NITRATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDreyfus, 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
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: antibody CR9114 heavy chain
L: antibody CR9114 light chain
A: antibody CR9114 heavy chain
B: antibody CR9114 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,08513
Polymers94,5274
Non-polymers5589
Water6,503361
1
H: antibody CR9114 heavy chain
L: antibody CR9114 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6989
Polymers47,2632
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-4 kcal/mol
Surface area19360 Å2
MethodPISA
2
A: antibody CR9114 heavy chain
B: antibody CR9114 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3874
Polymers47,2632
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-20 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.332, 141.667, 70.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11L-464-

HOH

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Components

#1: Antibody antibody CR9114 heavy chain


Mass: 24423.191 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody antibody CR9114 light chain


Mass: 22840.172 Da / Num. of mol.: 2 / Fragment: Fab Lambda
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M lithium nitrate, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2011
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: 2.05→50 Å / Num. all: 51891 / Num. obs: 51891 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.05→2.15 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→43.061 Å / SU ML: 0.63 / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 2645 5.1 %RANDOM
Rwork0.1996 ---
obs0.2021 51830 95.69 %-
all-51891 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.668 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2514 Å20 Å2-0 Å2
2--1.0859 Å20 Å2
3----4.3373 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 36 361 6846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126678
X-RAY DIFFRACTIONf_angle_d1.2879088
X-RAY DIFFRACTIONf_dihedral_angle_d15.9052365
X-RAY DIFFRACTIONf_chiral_restr0.0811025
X-RAY DIFFRACTIONf_plane_restr0.0061171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08760.33461170.2832446X-RAY DIFFRACTION91
2.0876-2.12780.30931510.26682581X-RAY DIFFRACTION97
2.1278-2.17120.3141490.2662553X-RAY DIFFRACTION97
2.1712-2.21840.33351380.26242549X-RAY DIFFRACTION96
2.2184-2.270.28761480.24842547X-RAY DIFFRACTION96
2.27-2.32680.30281300.26452562X-RAY DIFFRACTION96
2.3268-2.38970.29281470.2562530X-RAY DIFFRACTION95
2.3897-2.460.31671390.24992559X-RAY DIFFRACTION95
2.46-2.53940.32481420.25342532X-RAY DIFFRACTION95
2.5394-2.63010.31621360.25042557X-RAY DIFFRACTION95
2.6301-2.73540.25461270.23692546X-RAY DIFFRACTION94
2.7354-2.85990.30981410.2222510X-RAY DIFFRACTION94
2.8599-3.01060.29071290.21262556X-RAY DIFFRACTION94
3.0106-3.19920.27451290.2022525X-RAY DIFFRACTION93
3.1992-3.44610.23361290.1872555X-RAY DIFFRACTION94
3.4461-3.79270.25121360.16442657X-RAY DIFFRACTION97
3.7927-4.34110.16841540.14322725X-RAY DIFFRACTION100
4.3411-5.46760.15621520.13122788X-RAY DIFFRACTION100
5.4676-43.0710.21891510.17762907X-RAY DIFFRACTION100

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