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- PDB-7uvj: Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2 -

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Basic information

Entry
Database: PDB / ID: 7uvj
TitleRationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2
ComponentsApolipoprotein E
KeywordsDE NOVO PROTEIN / Immunogen / SARS-COV-2 / Viral epitope / scaffold
Function / homology
Function and homology information


lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process ...lipid transport involved in lipid storage / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / triglyceride-rich lipoprotein particle clearance / discoidal high-density lipoprotein particle / lipoprotein particle / negative regulation of triglyceride metabolic process / negative regulation of cholesterol biosynthetic process / regulation of amyloid-beta clearance / positive regulation of lipoprotein transport / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / chylomicron remnant clearance / chylomicron remnant / intermediate-density lipoprotein particle / maintenance of location in cell / very-low-density lipoprotein particle remodeling / acylglycerol homeostasis / NMDA glutamate receptor clustering / response to caloric restriction / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron clearance / positive regulation of phospholipid efflux / very-low-density lipoprotein particle clearance / Chylomicron remodeling / lipid transporter activity / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / cellular response to lipoprotein particle stimulus / positive regulation of low-density lipoprotein particle receptor catabolic process / regulation of amyloid fibril formation / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / regulation of protein metabolic process / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / AMPA glutamate receptor clustering / lipoprotein catabolic process / melanosome organization / multivesicular body, internal vesicle / reverse cholesterol transport / positive regulation of amyloid-beta clearance / positive regulation by host of viral process / high-density lipoprotein particle assembly / low-density lipoprotein particle / protein import / lipoprotein biosynthetic process / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol catabolic process / low-density lipoprotein particle remodeling / heparan sulfate proteoglycan binding / regulation of Cdc42 protein signal transduction / amyloid precursor protein metabolic process / negative regulation of amyloid fibril formation / triglyceride homeostasis / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / synaptic transmission, cholinergic / HDL remodeling / negative regulation of endothelial cell migration / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / Scavenging by Class A Receptors / triglyceride metabolic process / positive regulation of dendritic spine development / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / regulation of innate immune response / virion assembly / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / locomotory exploration behavior / antioxidant activity / positive regulation of endocytosis / lipoprotein particle binding / response to dietary excess / negative regulation of blood vessel endothelial cell migration / regulation of neuronal synaptic plasticity / negative regulation of long-term synaptic potentiation / negative regulation of platelet activation / positive regulation of dendritic spine maintenance / negative regulation of blood coagulation / positive regulation of cholesterol efflux / negative regulation of MAP kinase activity / long-term memory / negative regulation of protein secretion / fatty acid homeostasis / regulation of protein-containing complex assembly / synaptic cleft / long-chain fatty acid transport / intracellular transport
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Apolipoprotein E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsYennawar, N.H. / Vishweshwaraiah, Y.L. / Dokholyan, N.V.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD02858901 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134864 United States
Passan Foundation United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG071675 United States
Citation
#1: Journal: Biorxiv / Year: 2022
Title: Adaptation-proof SARS-CoV-2 vaccine design.
Authors: Vishweshwaraiah, Y.L. / Hnath, B. / Rackley, B. / Wang, J. / Gontu, A. / Chandler, M. / Afonin, K.A. / Kuchipudi, S.V. / Christensen, N. / Yennawar, N.H. / Dokholyan, N.V.
#2: Journal: Adv Funct Mater / Year: 2022
Title: Adaptation-Proof SARS-CoV-2 Vaccine Design
Authors: Vishweshwaraiah, Y.L. / Hnath, B. / Rackley, B. / Wang, J. / Gontu, A. / Chandler, M. / Afonin, K.A. / Kuchipudi, S.V. / Christensen, N. / Yennawar, N.H. / Dokholyan, N.V.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein E
B: Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3707
Polymers33,9142
Non-polymers4555
Water5,080282
1
A: Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2144
Polymers16,9571
Non-polymers2573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apolipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1553
Polymers16,9571
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.060, 95.631, 40.916
Angle α, β, γ (deg.)90.000, 108.576, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Apolipoprotein E / Apo-E / ED1


Mass: 16957.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: APOE / Production host: Escherichia coli (E. coli) / References: UniProt: P02649
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.99→95.63 Å / Num. obs: 18932 / % possible obs: 97 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.59 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.066 / Net I/σ(I): 4.87
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.216 / Num. unique obs: 1843 / CC1/2: 0.902 / Rpim(I) all: 0.133

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BZ4

1bz4


Resolution: 1.99→17.87 Å / SU ML: 0.3181 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.8594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3116 1848 9.83 %
Rwork0.263 16955 -
obs0.2678 18803 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 1.99→17.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 30 282 2662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212409
X-RAY DIFFRACTIONf_angle_d0.48133224
X-RAY DIFFRACTIONf_chiral_restr0.0294351
X-RAY DIFFRACTIONf_plane_restr0.003421
X-RAY DIFFRACTIONf_dihedral_angle_d12.3513943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.33881290.27121238X-RAY DIFFRACTION91.19
2.05-2.110.30941470.26911323X-RAY DIFFRACTION99.59
2.11-2.170.3331470.28231352X-RAY DIFFRACTION99.47
2.17-2.250.32511500.25911325X-RAY DIFFRACTION99.26
2.25-2.340.33131390.25581321X-RAY DIFFRACTION98.85
2.34-2.450.31341480.25571342X-RAY DIFFRACTION98.87
2.45-2.580.32151530.2681317X-RAY DIFFRACTION98.59
2.58-2.740.32391410.27031341X-RAY DIFFRACTION98.15
2.74-2.950.3561440.27351311X-RAY DIFFRACTION98.24
2.95-3.240.27751460.25291328X-RAY DIFFRACTION97.94
3.24-3.710.29561380.24121281X-RAY DIFFRACTION95.11
3.71-4.650.26861300.23911215X-RAY DIFFRACTION89.19
4.66-17.870.32031360.30531261X-RAY DIFFRACTION91.61
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)
11.13426178457-0.3609583220140.1094473922053.25709324221-2.019647837181.503720283640.0501563037309-0.207096715438-0.312641844310.30658535155-0.358586040583-0.7011424449480.1279728221581.018747416190.3084824769970.5344895747270.139699122791-0.03564384222980.8718294977460.0113948821140.5600633961884.16931729613-18.1904912226-7.93988774397
24.16332887616-0.7164288924111.586842748081.01956562732-0.2094885080681.809015403660.1132603749770.123159799435-0.1887510196880.03844697567130.12317669342-0.03895978369820.1587994590650.109592187237-0.129245618220.08216423022030.05112826913620.01739539083610.0688122403261-0.04307657527860.12129843429913.9676734672-8.76607825677-2.09392740069
34.01146000565-0.3804995752850.7571072431911.39660878171-0.1919964423921.19126483113-0.06871720187080.1020320411260.3800428758160.02015948649830.136966222828-0.190431287307-0.09758361111470.211804220689-0.02147356760240.02453431527730.03258582867560.04940024527090.116916182040.006858325628220.20620197587613.1006207297-1.27201412515-3.32995749989
44.7896598688-3.820474357550.1289557503544.44124310754-2.532026483124.35880144803-0.110462476146-0.394503663208-0.184305492810.238740132253-0.193898759053-0.577960700015-0.1427963940340.7324474260520.2787018622890.478290672038-0.0482070353227-0.1964507920570.6972685665460.07947684998720.731802131566-16.8424050834-11.7418746122-14.4478849125
50.840441762692-0.04665848965080.3327400798160.889928091026-0.07833456767170.432331147542-0.0438569661320.002457439600760.0892897649544-0.0214951501465-0.0125390256626-0.0016821921475-0.02144645862790.01503618026120.00222296676430.08947926690640.0425897101518-0.00640067999486-0.03742642643990.03593600937320.1424169258463.49981401476-1.492861041653.41246415333
61.63094045164-0.8977527278910.1711222000120.9759714963050.6573328942981.20724176371-0.107238249451-0.561529830530.7007340719761.27307706954-0.313188882427-0.543569117452-0.56857733690.008551196211440.4145153953880.808261003688-0.0314935115713-0.08477294401420.676638480734-0.05824094756130.76234815028223.522631377610.048294421619.0348286573
73.980558611221.698388476072.742478881361.68125839370.9192682340632.999040786140.0843467324054-0.141305990413-0.04920269147520.158334757962-0.1845047983770.01352663858430.145677475758-0.009417656889460.02698039958320.0856279164316-0.01792078861410.02948902807780.004500051964910.0087948051240.1584536528546.39114378076-9.294790621746.40560010424
81.51030497897-0.674965368865-0.05008289727491.330723433220.08958769796260.578013132180.08618576887710.128310559316-0.106058602425-0.0850903306820.02702432751770.172167068092-0.0504744192-0.0984628213024-0.01701541385550.1085881631870.042178526327-0.08673042392530.03458354683230.05076249384260.203767804036.35134021716.7685183564-3.27166806377
90.1352106594510.2558453207250.2140556765990.4873482721620.3901706878490.394769786451-0.13531374124-0.346651171279-0.02810313930060.001502004267010.03905895634490.0589202328847-0.103762428306-0.1418202103990.1010347038880.8008651732840.5304364133690.1798718464511.171471661120.05980973489020.76984215577735.454194062525.8096410689-13.9455481416
103.376057579871.57039833427-1.079337603611.78098604401-0.428662615520.981940234153-0.02417584756010.02272032105480.000671945573308-0.0423661988652-0.0522946902770.04344410225090.0211450961623-0.02891702018730.02862884695070.0286352665798-0.0200655026389-0.0391689464089-0.01496119228160.01456579562330.16587145001315.932431607913.96183443393.30414514353
115.279752169592.368811077570.5524966056658.034516094654.409853951362.54249405556-0.0399727483569-0.363019260571-0.458746134682-0.154685791779-0.5230964313510.5376550990230.121351443726-1.259190592180.5557328705120.536806994732-0.167482297308-0.09010826850590.521448828742-0.006668642697890.330024669927-7.393557844445.3466341840317.7161384966
125.67000731942.43668078639-4.274372089491.79874215385-1.968860112694.770914186070.0715207496714-0.173635630618-0.03299187278730.0441440992884-0.188601827568-0.161340401279-0.1661736576480.02144704506420.05581702110880.05740812330410.00593791120004-0.02372916684270.01441042885130.02485511576090.12533213867613.569648775322.01359915615.99704748448
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 25 )AA20 - 251 - 6
22chain 'A' and (resid 26 through 43 )AA26 - 437 - 24
33chain 'A' and (resid 44 through 79 )AA44 - 7925 - 60
44chain 'A' and (resid 80 through 90 )AA80 - 9061 - 71
55chain 'A' and (resid 91 through 124 )AA91 - 12472 - 105
66chain 'A' and (resid 125 through 130 )AA125 - 130106 - 111
77chain 'A' and (resid 131 through 166 )AA131 - 166112 - 147
88chain 'B' and (resid 23 through 79 )BE23 - 791 - 57
99chain 'B' and (resid 80 through 90 )BE80 - 9058 - 68
1010chain 'B' and (resid 91 through 124 )BE91 - 12469 - 102
1111chain 'B' and (resid 125 through 131 )BE125 - 131103 - 109
1212chain 'B' and (resid 132 through 166 )BE132 - 166110 - 144

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