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- PDB-5tr8: Crystal structure of vaccine-elicited pan- influenza H1N1 neutral... -

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Basic information

Entry
Database: PDB / ID: 5tr8
TitleCrystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6.
Components
  • 441D6 Fab Heavy chain
  • 441D6 Fab Light chain
KeywordsIMMUNE SYSTEM / Nanoparticle / Ferritin / Antibody
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / MAb 44B1 heavy chain / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsJoyce, M.G. / Kanekiyo, M. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
CitationJournal: Nat Immunol / Year: 2019
Title: Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses.
Authors: Masaru Kanekiyo / M Gordon Joyce / Rebecca A Gillespie / John R Gallagher / Sarah F Andrews / Hadi M Yassine / Adam K Wheatley / Brian E Fisher / David R Ambrozak / Adrian Creanga / Kwanyee ...Authors: Masaru Kanekiyo / M Gordon Joyce / Rebecca A Gillespie / John R Gallagher / Sarah F Andrews / Hadi M Yassine / Adam K Wheatley / Brian E Fisher / David R Ambrozak / Adrian Creanga / Kwanyee Leung / Eun Sung Yang / Seyhan Boyoglu-Barnum / Ivelin S Georgiev / Yaroslav Tsybovsky / Madhu S Prabhakaran / Hanne Andersen / Wing-Pui Kong / Ulrich Baxa / Kathryn L Zephir / Julie E Ledgerwood / Richard A Koup / Peter D Kwong / Audray K Harris / Adrian B McDermott / John R Mascola / Barney S Graham /
Abstract: The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new ...The present vaccine against influenza virus has the inevitable risk of antigenic discordance between the vaccine and the circulating strains, which diminishes vaccine efficacy. This necessitates new approaches that provide broader protection against influenza. Here we designed a vaccine using the hypervariable receptor-binding domain (RBD) of viral hemagglutinin displayed on a nanoparticle (np) able to elicit antibody responses that neutralize H1N1 influenza viruses spanning over 90 years. Co-display of RBDs from multiple strains across time, so that the adjacent RBDs are heterotypic, provides an avidity advantage to cross-reactive B cells. Immunization with the mosaic RBD-np elicited broader antibody responses than those induced by an admixture of nanoparticles encompassing the same set of RBDs as separate homotypic arrays. Furthermore, we identified a broadly neutralizing monoclonal antibody in a mouse immunized with mosaic RBD-np. The mosaic antigen array signifies a unique approach that subverts monotypic immunodominance and allows otherwise subdominant cross-reactive B cell responses to emerge.
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 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 1.4Nov 20, 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
L: 441D6 Fab Light chain
H: 441D6 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6914
Polymers47,5742
Non-polymers1172
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-43 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.463, 83.332, 83.160
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-518-

HOH

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Components

#1: Antibody 441D6 Fab Light chain


Mass: 23694.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / References: UniProt: Q7TS98
#2: Antibody 441D6 Fab Heavy chain


Mass: 23879.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Homo sapiens (human) / References: UniProt: A0A0E4B366
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 12% PEG3350, 100 mM HEPES pH 7.5, 5 mM MgCl2, 5mM NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→24.607 Å / Num. obs: 42733 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.57
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.49 / CC1/2: 0.718 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPT

4zpt


Resolution: 2.01→24.607 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 2053 4.9 %
Rwork0.1743 --
obs0.1756 41925 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→24.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 2 248 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053420
X-RAY DIFFRACTIONf_angle_d0.8564649
X-RAY DIFFRACTIONf_dihedral_angle_d14.7652038
X-RAY DIFFRACTIONf_chiral_restr0.053514
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0105-2.05720.30911130.30162138X-RAY DIFFRACTION80
2.0572-2.10870.33921290.29432595X-RAY DIFFRACTION96
2.1087-2.16560.26761320.26122708X-RAY DIFFRACTION99
2.1656-2.22930.27181560.24912720X-RAY DIFFRACTION100
2.2293-2.30120.35851250.30072698X-RAY DIFFRACTION98
2.3012-2.38340.29911370.22552679X-RAY DIFFRACTION100
2.3834-2.47880.22971310.21472744X-RAY DIFFRACTION100
2.4788-2.59150.2411350.20272714X-RAY DIFFRACTION100
2.5915-2.72790.25111410.22693X-RAY DIFFRACTION100
2.7279-2.89860.21111330.18722750X-RAY DIFFRACTION100
2.8986-3.1220.2161650.18272702X-RAY DIFFRACTION100
3.122-3.43540.17251310.16472726X-RAY DIFFRACTION100
3.4354-3.93080.18521420.14642731X-RAY DIFFRACTION99
3.9308-4.94580.14131390.12432732X-RAY DIFFRACTION99
4.9458-24.60890.1681440.15982542X-RAY DIFFRACTION92
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)
14.19240.41363.31952.34562.00366.7570.1008-0.1002-0.37720.15620.0379-0.01150.47880.1816-0.12250.4558-0.04140.07580.41960.05330.378148.06837.0549-16.8063
22.60961.55760.3735.79661.04314.4878-0.0401-0.6023-0.19530.1125-0.2510.65740.0917-0.62510.24810.360.01730.11490.4901-0.0280.399242.16910.957-15.0897
34.88661.87154.42191.79152.50364.6043-0.0043-0.2488-0.43960.0627-0.01660.10240.2820.0630.1170.4144-0.12560.01350.2910.01350.418339.6052.3828-35.7845
44.33762.3591-2.14545.4863-3.01954.96820.17070.36140.3171-0.17360.22630.4762-0.4712-0.3126-0.43320.40670.0163-0.04470.2839-0.02010.328942.287118.4412-56.2246
52.09611.2222-2.02433.8376-2.50437.1779-0.01250.1999-0.1647-0.2875-0.0998-0.07530.21020.27820.150.30660.012-0.04730.3234-0.02150.388647.060810.7726-54.3106
63.7973-0.4443-2.32112.22290.72457.30620.0384-0.08780.3870.435-0.01150.6196-0.8099-0.8064-0.14670.66470.23610.05720.5408-0.0510.64543.399834.7325-18.3233
74.35292.09982.00128.1071-1.94562.95660.1845-0.48380.14130.6231-0.1005-0.3814-0.1920.4568-0.13690.3940.0550.01790.4059-0.04760.305151.62327.6415-14.7978
82.1368-0.03671.07391.9633-0.69694.0572-0.05-0.34560.21960.481-0.03940.1913-0.5120.06970.03850.45940.08880.02330.3346-0.09720.39449.737631.737-19.6007
93.54733.8952-1.95715.5527-0.74973.2885-0.2260.7204-0.5479-0.79340.21330.26470.1346-0.81630.06470.46490.0103-0.14640.4554-0.07850.577135.594119.739-59.0297
103.58980.85950.7325.68631.30353.5404-0.01940.0153-0.0264-0.2081-0.12160.7194-0.0884-0.43020.11560.26960.0426-0.03770.26210.01560.417836.315824.521-48.7372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'L' and (resid 39 through 101 )
3X-RAY DIFFRACTION3chain 'L' and (resid 102 through 113 )
4X-RAY DIFFRACTION4chain 'L' and (resid 114 through 139 )
5X-RAY DIFFRACTION5chain 'L' and (resid 140 through 212 )
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 33 )
7X-RAY DIFFRACTION7chain 'H' and (resid 34 through 59 )
8X-RAY DIFFRACTION8chain 'H' and (resid 60 through 119 )
9X-RAY DIFFRACTION9chain 'H' and (resid 120 through 134 )
10X-RAY DIFFRACTION10chain 'H' and (resid 135 through 215 )

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