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- PDB-4m5z: Crystal structure of broadly neutralizing antibody 5J8 bound to 2... -

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Basic information

Entry
Database: PDB / ID: 4m5z
TitleCrystal structure of broadly neutralizing antibody 5J8 bound to 2009 pandemic influenza hemagglutinin, HA1 subunit
Components
  • Fab 5J8 heavy chain
  • Fab 5J8 light chain
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / immunoglobulin fold / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHong, M. / Lee, P.S. / Wilson, I.A.
CitationJournal: J Virol / Year: 2013
Title: Antibody recognition of the pandemic H1N1 Influenza virus hemagglutinin receptor binding site.
Authors: Minsun Hong / Peter S Lee / Ryan M B Hoffman / Xueyong Zhu / Jens C Krause / Nick S Laursen / Sung-Il Yoon / Langzhou Song / Lynda Tussey / James E Crowe / Andrew B Ward / Ian A Wilson
Abstract: Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in ...Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
H: Fab 5J8 heavy chain
L: Fab 5J8 light chain


Theoretical massNumber of molelcules
Total (without water)72,7393
Polymers72,7393
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.549, 67.549, 259.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 24890.957 Da / Num. of mol.: 1 / Fragment: UNP residues 63-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: G8XMJ2
#2: Antibody Fab 5J8 heavy chain


Mass: 25088.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody Fab 5J8 light chain


Mass: 22760.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 23% PEG8000, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 11, 2012
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM) with indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 33082 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2526 / Rsym value: 0.755 / % possible all: 83.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M5Y CHAINS H AND L

4m5y


Resolution: 2.25→48.466 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1667 5.05 %RANDOM
Rwork0.1905 ---
obs0.193 32999 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 0 90 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015067
X-RAY DIFFRACTIONf_angle_d1.5496901
X-RAY DIFFRACTIONf_dihedral_angle_d14.2921800
X-RAY DIFFRACTIONf_chiral_restr0.093761
X-RAY DIFFRACTIONf_plane_restr0.01881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31620.30251090.28232210X-RAY DIFFRACTION85
2.3162-2.3910.31111300.25682434X-RAY DIFFRACTION93
2.391-2.47650.29791450.24392588X-RAY DIFFRACTION99
2.4765-2.57560.28141400.24432598X-RAY DIFFRACTION100
2.5756-2.69280.31241320.24082660X-RAY DIFFRACTION100
2.6928-2.83480.31461380.23622635X-RAY DIFFRACTION100
2.8348-3.01240.27031480.23292619X-RAY DIFFRACTION100
3.0124-3.24490.30491410.22492675X-RAY DIFFRACTION100
3.2449-3.57130.26181390.20362663X-RAY DIFFRACTION99
3.5713-4.08790.23071520.18022651X-RAY DIFFRACTION100
4.0879-5.14940.18491490.14522731X-RAY DIFFRACTION99
5.1494-48.47730.20461440.16942868X-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)
13.51480.52671.47131.3660.33673.440.0368-0.6047-0.44740.18730.38210.09930.329-0.8808-0.37110.7338-0.1218-0.23310.71670.26490.5658-15.4755-24.2632-33.0124
21.6637-0.0890.10980.95710.11151.39430.3014-0.1967-0.11330.13120.04750.20940.5062-0.6423-0.01420.4765-0.6506-0.07390.82820.33490.4237-25.234-8.9098-68.7175
31.0222-0.8918-0.67333.29311.17422.3725-0.04940.3099-0.1823-0.1617-0.10990.1530.017-0.42650.15910.3084-0.1544-0.00550.69640.11160.3767-22.8399-12.8084-99.7645
42.46340.1479-0.90121.41080.54542.99440.2803-0.29-0.09070.4405-0.0456-0.44050.41850.2862-0.18860.6182-0.4018-0.24120.72930.21810.5129-6.4596-18.8235-66.5548
53.6639-1.34031.39723.3208-0.44763.20950.10470.3074-0.0309-0.14920.0672-0.3082-0.0816-0.0704-0.15840.2863-0.14750.00980.66550.10330.4271-7.0133-10.7036-105.2643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA55 - 312
2X-RAY DIFFRACTION2chain H and resid 1:123H1 - 123
3X-RAY DIFFRACTION3chain H and resid 124:209H124 - 209
4X-RAY DIFFRACTION4chain L and resid 1:109L1 - 109
5X-RAY DIFFRACTION5chain L and resid 110:209L110 - 209

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