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- PDB-6v8e: Computationally designed C3-symmetric homotrimer from TPR repeat ... -

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Entry
Database: PDB / ID: 6v8e
TitleComputationally designed C3-symmetric homotrimer from TPR repeat protein
ComponentsDesigned proteinDesign
KeywordsDE NOVO PROTEIN / designed trimers / designed nanoparticles / ribosome-binding site
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSankaran, B. / Ueda, G. / Zwart, P.H. / Baker, D.
Funding support United States, 5items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1120319, OPP11157823, OPP1156262, OPP1115782, OPP1084519 United States
National Science Foundation (NSF, United States)NSF CHE 1629214 United States
National Institutes of Health/Office of the DirectorP41 GM103403-10 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 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
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed protein
B: Designed protein
C: Designed protein
D: Designed protein
E: Designed protein
F: Designed protein


Theoretical massNumber of molelcules
Total (without water)82,8426
Polymers82,8426
Non-polymers00
Water1,51384
1
A: Designed protein
B: Designed protein
C: Designed protein


Theoretical massNumber of molelcules
Total (without water)41,4213
Polymers41,4213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-30 kcal/mol
Surface area17260 Å2
MethodPISA
2
D: Designed protein
E: Designed protein
F: Designed protein


Theoretical massNumber of molelcules
Total (without water)41,4213
Polymers41,4213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-27 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.470, 64.910, 99.030
Angle α, β, γ (deg.)90.00, 106.33, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Designed protein / Design


Mass: 13807.026 Da / Num. of mol.: 6
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 / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1M LiCl 100mM citrate 20% w/v PEG 6000 pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→38.9 Å / Num. obs: 28508 / % possible obs: 99.83 % / Redundancy: 4.6 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1427 / Rpim(I) all: 0.07334 / Rrim(I) all: 0.1608 / Net I/σ(I): 9.5
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.8023 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 2836 / CC1/2: 0.729 / CC star: 0.918 / Rpim(I) all: 0.4106 / Rrim(I) all: 0.9033 / % possible all: 99.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Coot1.17.1_3660model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: designed model from rosetta

Resolution: 2.53→38.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 22.749 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.279
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23166 1442 5.1 %RANDOM
Rwork0.18591 ---
obs0.18821 27066 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 51.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.79 Å2
2---0.2 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.53→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 84 5932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195987
X-RAY DIFFRACTIONr_bond_other_d0.0010.025144
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.8948110
X-RAY DIFFRACTIONr_angle_other_deg1.2252.93311984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1055706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72425.806372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13915978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4081524
X-RAY DIFFRACTIONr_chiral_restr0.0980.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021239
X-RAY DIFFRACTIONr_mcbond_it4.4072.3922836
X-RAY DIFFRACTIONr_mcbond_other4.4072.3912834
X-RAY DIFFRACTIONr_mcangle_it5.9983.583535
X-RAY DIFFRACTIONr_mcangle_other5.9973.583535
X-RAY DIFFRACTIONr_scbond_it6.9552.9583151
X-RAY DIFFRACTIONr_scbond_other6.9542.9583152
X-RAY DIFFRACTIONr_scangle_other9.6184.2254575
X-RAY DIFFRACTIONr_long_range_B_refined10.89428.9837170
X-RAY DIFFRACTIONr_long_range_B_other10.89628.9287157
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 103 -
Rwork0.273 2030 -
obs--99.91 %
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)
13.1744-0.3177-1.17023.2054-0.65634.29590.0040.2740.0458-0.2581-0.052-0.23770.15390.01270.0480.3054-0.0081-0.11260.02760.01220.079421.3582.6585.376
23.131.01050.98033.75810.76985.88670-0.0852-0.30050.11120.0601-0.6756-0.02980.9625-0.06010.3167-0.0003-0.06470.17930.0170.150239.02911.52735.834
32.09760.8446-0.87873.2431-1.08211.4953-0.01040.01560.08420.05370.09230.2037-0.1637-0.1375-0.08190.41750.0254-0.0820.0456-0.00120.033214.443-14.07638.05
44.0213-1.18220.74855.8281-0.69093.3066-0.1574-0.18660.36990.2044-0.0122-0.8523-0.08330.3960.16950.36490.0067-0.08980.08840.00020.144331.299-28.6928.043
52.9897-0.0403-0.55552.11971.04644.98660.04290.31530.1671-0.25420.0965-0.2172-0.21090.1143-0.13930.3218-0.0012-0.07240.04460.01620.115420.804-37.56-5.834
62.8279-1.2019-0.60993.86980.27130.5717-0.0377-0.0737-0.12790.0770.07330.2030.0549-0.053-0.03560.2977-0.0061-0.11430.01550.01430.0652.683-11.89111.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B1 - 117
3X-RAY DIFFRACTION3C1 - 119
4X-RAY DIFFRACTION4D1 - 118
5X-RAY DIFFRACTION5E1 - 118
6X-RAY DIFFRACTION6F1 - 119

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