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

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Basic information

Entry
Database: PDB / ID: 4fqv
TitleCrystal structure of broadly neutralizing antibody CR9114 bound to H7 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: 5.75 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
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
H: Antibody CR9114 heavy chain
L: Antibody CR9114 light chain
I: Antibody CR9114 heavy chain
M: Antibody CR9114 light chain
J: Antibody CR9114 heavy chain
N: Antibody CR9114 light chain


Theoretical massNumber of molelcules
Total (without water)307,96912
Polymers307,96912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.570, 197.570, 223.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 35894.434 Da / Num. of mol.: 3 / Fragment: UNP residues 26-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Netherlands/219/2003 (H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q6VMK1
#2: Protein Hemagglutinin HA2 / hemagglutinin membrane fusion subunit HA2


Mass: 20327.314 Da / Num. of mol.: 3 / Fragment: UNP residues 349-524
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Netherlands/219/2003 (H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q6VMK1
#3: Antibody Antibody CR9114 heavy chain


Mass: 23594.311 Da / Num. of mol.: 3 / 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.: 3
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)
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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 1 M lithium chloride, 10% PEG6000, and 100 mM MES, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 5.75→50 Å / Num. obs: 13125 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rsym value: 0.14 / Net I/σ(I): 18
Reflection shellResolution: 5.75→5.82 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.87 / % possible all: 97.7

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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: 5.75→49.354 Å / SU ML: 1.1 / σ(F): 1.34 / Phase error: 46.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3393 642 4.93 %RANDOM
Rwork0.314 ---
obs0.3152 13028 99.4 %-
Solvent computationShrinkage radii: 1.4 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.75→49.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20902 0 0 0 20902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621412
X-RAY DIFFRACTIONf_angle_d1.20929018
X-RAY DIFFRACTIONf_dihedral_angle_d16.8047732
X-RAY DIFFRACTIONf_chiral_restr0.0813196
X-RAY DIFFRACTIONf_plane_restr0.0073807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.75-6.19350.451280.42142381X-RAY DIFFRACTION98
6.1935-6.81530.38651460.38512408X-RAY DIFFRACTION100
6.8153-7.79820.36781120.35332471X-RAY DIFFRACTION100
7.7982-9.81220.32191170.31562506X-RAY DIFFRACTION100
9.8122-49.35530.32151390.28312620X-RAY DIFFRACTION99
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)
11.5385-0.14571.44252.4041.12562.11161.86674.94271.3112-2.1381-0.642-2.03670.99921.43590.89495.30241.5190.55553.4070.6612.0347-9.843971.1638-75.2751
21.12920.52130.17971.81010.3821.04530.91780.82910.62260.0387-0.1938-0.9502-0.12570.80760.96692.07920.0294-0.5852-0.2588-0.25882.1832-9.344667.1578-24.1476
31.78380.3882-0.322.0885-0.16910.47740.46161.2542-1.1342-4.5256-0.04340.91021.1888-0.1449-0.63856.08160.7683-1.6042.9078-0.56872.4039-22.162741.3621-75.0003
41.53090.2357-0.27623.6215-0.02431.59230.74890.8192-0.56350.7605-0.71170.2358-0.2809-0.24480.24651.3646-0.0664-0.83430.2402-0.54932.2911-11.340145.778-24.8306
51.9131-1.062-1.250.57340.95972.17861.01691.83110.9337-0.9914-0.0762-0.349-2.2868-1.4252.12263.69460.3104-0.13542.68170.55111.6186-41.434366.7897-70.3244
61.863-0.8392-0.29511.66450.23541.65910.2262-1.12530.9577-0.88040.7960.4646-0.6059-1.22860.70271.45820.123-0.22771.4990.32841.1274-28.757458.0618-21.8118
70.2204-0.00560.31030.333-0.12440.7777-0.65690.74670.1914-0.1582-1.213-0.2820.44910.1587-1.29922.3682-0.8048-0.3754-0.0631.36393.832910.590183.4646-36.1926
80.58070.5671-0.53320.5159-0.51090.7523-1.5203-1.37940.5291-0.1926-0.7297-0.2835-1.02340.0001-1.09381.59130.1946-0.86823.3356-0.35774.574725.112978.6343-20.5973
90.67330.1290.3610.61480.03780.2262-0.4936-1.8736-0.09840.989-0.3444-0.2660.43710.5968-0.75241.05380.1617-0.01872.376-0.25620.6936-53.469371.2348-25.3441
100.0485-0.0360.13050.04910.15410.35750.0961-0.93160.05561.36140.4153-0.10351.34760.75760.55893.35730.8567-0.53372.09660.1174-0.3654-50.996782.9491-7.0318
111.00180.16080.74960.34110.00461.7918-1.1209-0.60861.1051-0.18710.10670.9141-1.0469-1.1127-1.51320.70050.21090.10620.6931-1.2001-0.2155-9.879919.6668-36.1729
120.7319-1.2167-0.41021.85850.50081.9431-0.9286-0.0022-0.56612.1021-1.27250.32320.4393-0.0746-2.05411.5284-0.43680.33691.34770.23091.112-15.269210.281-17.149
130.04210.0256-0.20940.2001-0.07840.37061.53710.0436-0.00680.3360.40461.0469-0.5592-0.24120.09152.6616-0.9444-0.57123.51720.75984.255435.253482.3413-56.8683
140.01180.04970.03151.22530.81680.7392-0.35431.41210.0709-1.6746-0.44841.0125-1.1967-0.5276-0.21842.50760.2715-0.11732.98390.02154.641347.935690.5976-48.8589
150.2176-0.01540.17520.2581-0.04920.1582-0.3007-0.2077-0.5192-0.0730.28410.01930.16091.0737-0.3833-0.38150.2990.841.96080.3571.1113-71.622899.1976-38.2242
160.63140.07540.12110.7105-0.14580.3842-0.20170.44660.22790.46370.0381-1.18550.45950.2008-0.38551.42670.891-0.39491.7825-0.2081.3493-80.3378101.1132-23.6166
170.2951-0.1185-0.07510.41120.17210.14130.77740.418-0.0464-1.0163-0.34150.27730.2198-1.20310.52861.05061.1873-0.86251.1143-0.82162.0247-25.8495-9.0865-51.8333
180.35460.1277-0.20320.2931-0.13160.65860.70940.5752-0.2453-0.3167-0.9197-0.35630.2624-0.5366-0.72591.47760.40750.07851.43610.17950.7028-17.3828-20.0581-41.7991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain H and resid 1:113
8X-RAY DIFFRACTION8chain L and resid 2:107
9X-RAY DIFFRACTION9chain I and resid 1:113
10X-RAY DIFFRACTION10chain M and resid 2:107
11X-RAY DIFFRACTION11chain J and resid 1:113
12X-RAY DIFFRACTION12chain N and resid 2:107
13X-RAY DIFFRACTION13chain H and resid 114:213
14X-RAY DIFFRACTION14chain L and resid 108:208
15X-RAY DIFFRACTION15chain I and resid 114:213
16X-RAY DIFFRACTION16chain M and resid 108:208
17X-RAY DIFFRACTION17chain J and resid 114:213
18X-RAY DIFFRACTION18chain N and resid 108:208

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