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- PDB-6veh: Computationally designed C3-symmetric homotrimer from HEAT repeat... -

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Basic information

Entry
Database: PDB / ID: 6veh
TitleComputationally designed C3-symmetric homotrimer from HEAT repeat protein
ComponentsHEAT repeat domain-containing protein
KeywordsDE NOVO PROTEIN / designed protein / vaccine
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.303 Å
AuthorsBick, M.J. / Ueda, G. / Baker, D.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD018483 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2020
Title: Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens.
Authors: George Ueda / Aleksandar Antanasijevic / Jorge A Fallas / William Sheffler / Jeffrey Copps / Daniel Ellis / Geoffrey B Hutchinson / Adam Moyer / Anila Yasmeen / Yaroslav Tsybovsky / Young- ...Authors: George Ueda / Aleksandar Antanasijevic / Jorge A Fallas / William Sheffler / Jeffrey Copps / Daniel Ellis / Geoffrey B Hutchinson / Adam Moyer / Anila Yasmeen / Yaroslav Tsybovsky / Young-Jun Park / Matthew J Bick / Banumathi Sankaran / Rebecca A Gillespie / Philip Jm Brouwer / Peter H Zwart / David Veesler / Masaru Kanekiyo / Barney S Graham / Rogier W Sanders / John P Moore / Per Johan Klasse / Andrew B Ward / Neil P King / David Baker /
Abstract: Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self- ...Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT repeat domain-containing protein


Theoretical massNumber of molelcules
Total (without water)21,0221
Polymers21,0221
Non-polymers00
Water45025
1
A: HEAT repeat domain-containing protein

A: HEAT repeat domain-containing protein

A: HEAT repeat domain-containing protein


Theoretical massNumber of molelcules
Total (without water)63,0673
Polymers63,0673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4540 Å2
ΔGint-61 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.182, 88.182, 65.244
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HEAT repeat domain-containing protein


Mass: 21022.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1mM DL-glutamic acid monohydrate, 100mM DL-alanine, 100mM glycine, 100mM DL-lysine monohydrochloride, 100mM DL-serine, 100mM Tris (base), 100mM BICINE, 20% (v/v) ethylene glycol, 10 % (w/v) PEG 8000, pH8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 8361 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 40.43 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.055 / Rrim(I) all: 0.131 / Χ2: 0.944 / Net I/σ(I): 6.2 / Num. measured all: 46905
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3451.1983880.6190.5981.3410.714100
2.34-2.385.20.9484540.5860.4581.0530.673100
2.38-2.435.40.8454100.6530.40.9350.759100
2.43-2.485.60.8354230.780.3890.9210.715100
2.48-2.535.50.6174030.8050.290.6831.248100
2.53-2.595.70.6744240.7930.3120.7430.769100
2.59-2.665.70.5464180.8780.2530.6030.86100
2.66-2.735.70.4114120.9040.190.4530.95100
2.73-2.815.70.384300.9160.1750.4181.023100
2.81-2.95.70.2994270.9520.1380.331.003100
2.9-35.70.2793860.950.1280.3070.958100
3-3.125.70.2554310.9510.1170.281.03100
3.12-3.265.70.2284280.9650.1060.2511.004100
3.26-3.445.60.1524080.9730.070.1670.968100
3.44-3.655.70.144350.9870.0640.1540.985100
3.65-3.935.70.1244170.9840.0570.1371.005100
3.93-4.335.60.0884090.9930.0410.0970.993100
4.33-4.965.50.0674230.9950.0320.0741.059100
4.96-6.245.90.0594160.9970.0270.0651.039100
6.24-1005.80.0334190.9990.0150.0361.07799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000714ndata reduction
HKL-2000714ndata scaling
PHASER2.8.2phasing
PHENIXdev_3112refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.303→44.091 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2261 756 9.88 %
Rwork0.2021 --
obs0.2045 7654 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.21 Å2 / Biso mean: 53.4257 Å2 / Biso min: 26.15 Å2
Refinement stepCycle: final / Resolution: 2.303→44.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 25 1274
Biso mean---50.8 -
Num. residues----180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3035-2.48130.271280.2417121080
2.4813-2.7310.30521510.2316132189
2.731-3.12610.24671540.2119142994
3.1261-3.93820.20641570.1929144795
3.9382-44.0910.20851660.1919149199

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