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- PDB-8p4t: The spike complex of the Lujo Virus -

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Basic information

Entry
Database: PDB / ID: 8p4t
TitleThe spike complex of the Lujo Virus
Components(Glycoprotein) x 3
KeywordsVIRAL PROTEIN / Spike complex
Function / homologyArenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / host cell Golgi apparatus / viral envelope / membrane / Glycoprotein
Function and homology information
Biological speciesMammarenavirus lujoense
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsEilon-Ashkenazy, M. / Diskin, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation209/20 Israel
CitationJournal: To Be Published
Title: The spike complex of the Lujo Virus
Authors: Eilon-Ashkenazy, M. / Diskin, R.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein
a: Glycoprotein
SA: Glycoprotein
B: Glycoprotein
C: Glycoprotein
SB: Glycoprotein
SC: Glycoprotein
b: Glycoprotein
c: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,69340
Polymers161,3629
Non-polymers12,33131
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_1ens_2chain "SC"
d_2ens_2chain "SB"
d_3ens_2chain "SA"
d_1ens_3chain "a"
d_2ens_3chain "b"
d_3ens_3chain "c"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERMETMETAA60 - 2212 - 163
d_12ens_1NAGNAGNAGNAGDJ1
d_13ens_1NAGNAGNAGNAGDJ2
d_14ens_1FUCFUCFUCFUCDJ5
d_15ens_1BMABMABMABMADJ3
d_16ens_1MANMANMANMANDJ4
d_17ens_1NAGNAGNAGNAGAS301
d_18ens_1NAGNAGNAGNAGAT302
d_19ens_1NAGNAGNAGNAGEK1
d_110ens_1NAGNAGNAGNAGEK2
d_111ens_1BMABMABMABMAEK3
d_112ens_1MANMANMANMANEK4
d_113ens_1MANMANMANMANEK6
d_114ens_1MANMANMANMANEK5
d_115ens_1MANMANMANMANEK7
d_116ens_1NAGNAGNAGNAGAU303
d_117ens_1NAGNAGNAGNAGAV304
d_21ens_1SERSERMETMETBD60 - 2212 - 163
d_22ens_1NAGNAGNAGNAGGM1
d_23ens_1NAGNAGNAGNAGGM2
d_24ens_1FUCFUCFUCFUCGM5
d_25ens_1BMABMABMABMAGM3
d_26ens_1MANMANMANMANGM4
d_27ens_1NAGNAGNAGNAGBAA301
d_28ens_1NAGNAGNAGNAGBBA302
d_29ens_1NAGNAGNAGNAGHN1
d_210ens_1NAGNAGNAGNAGHN2
d_211ens_1BMABMABMABMAHN3
d_212ens_1MANMANMANMANHN4
d_213ens_1MANMANMANMANHN6
d_214ens_1MANMANMANMANHN5
d_215ens_1MANMANMANMANHN7
d_216ens_1NAGNAGNAGNAGBCA303
d_217ens_1NAGNAGNAGNAGBDA304
d_31ens_1SERSERMETMETCE60 - 2212 - 163
d_32ens_1NAGNAGNAGNAGIO1
d_33ens_1NAGNAGNAGNAGIO2
d_34ens_1FUCFUCFUCFUCIO5
d_35ens_1BMABMABMABMAIO3
d_36ens_1MANMANMANMANIO4
d_37ens_1NAGNAGNAGNAGCEA301
d_38ens_1NAGNAGNAGNAGCFA302
d_39ens_1NAGNAGNAGNAGJP1
d_310ens_1NAGNAGNAGNAGJP2
d_311ens_1BMABMABMABMAJP3
d_312ens_1MANMANMANMANJP4
d_313ens_1MANMANMANMANJP6
d_314ens_1MANMANMANMANJP5
d_315ens_1MANMANMANMANJP7
d_316ens_1NAGNAGNAGNAGCGA303
d_317ens_1NAGNAGNAGNAGCHA304
d_11ens_2VALVALLEULEUSCG2 - 355 - 38
d_21ens_2VALVALLEULEUSBF2 - 355 - 38
d_31ens_2VALVALLEULEUSAC2 - 355 - 38
d_11ens_3LYSLYSLEULEUaB222 - 4091 - 188
d_12ens_3NAGNAGNAGNAGFL1
d_13ens_3NAGNAGNAGNAGFL2
d_14ens_3NAGNAGNAGNAGaX501
d_15ens_3NAGNAGNAGNAGaY502
d_16ens_3NAGNAGNAGNAGaZ503
d_21ens_3LYSLYSLEULEUbH222 - 4091 - 188
d_22ens_3NAGNAGNAGNAGKQ1
d_23ens_3NAGNAGNAGNAGKQ2
d_24ens_3NAGNAGNAGNAGbIA501
d_25ens_3NAGNAGNAGNAGbJA502
d_26ens_3NAGNAGNAGNAGbKA503
d_31ens_3LYSLYSLEULEUcI222 - 4091 - 188
d_32ens_3NAGNAGNAGNAGLR1
d_33ens_3NAGNAGNAGNAGLR2
d_34ens_3NAGNAGNAGNAGcLA501
d_35ens_3NAGNAGNAGNAGcMA502
d_36ens_3NAGNAGNAGNAGcNA503

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.503139094725, -0.864204933257, -0.000940581411724), (0.864205437873, -0.503138651647, -0.000677030819402), (0.000111850510836, -0.00115349624435, 0.999999328468)249.717730982, 67.478983415, 0.0419937349826
2given(-0.495427261841, 0.868648853484, -0.000998781865525), (-0.868644754208, -0.495428040579, -0.00271064493871), (-0.00284942316082, -0.000475340771724, 0.999995827411)66.0899676023, 249.597618851, 0.407836228529
3given(-0.472970487685, 0.880581217771, 0.0295911589504), (-0.880883484378, -0.471892991556, -0.0368956836291), (-0.0185257854999, -0.0435169326826, 0.998880909739)58.1426103124, 252.763808855, 7.84855022776
4given(-0.47463284116, -0.880085993686, -0.013126683129), (0.880131447188, -0.474714568211, 0.0038359353347), (-0.00960738067439, -0.00973254573272, 0.999906483522)250.253597098, 61.8385331765, 2.39626392898
5given(-0.499280602055, -0.866431269272, -0.00396686774613), (0.866408513392, -0.499296271497, 0.00628658811179), (-0.00742753879225, -0.000298156489422, 0.999972371003)249.912577658, 66.1291408743, 0.613103617969
6given(-0.497045993223, 0.867723756962, -0.000873055144786), (-0.867719104823, -0.497046271906, -0.00292552720047), (-0.00297249825837, -0.00069655494436, 0.999995339522)66.5123571491, 249.768026286, 0.264449384506

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Components

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Protein , 3 types, 9 molecules ABCabcSASBSC

#1: Protein Glycoprotein


Mass: 19017.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus lujoense / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: C5ILC1
#2: Protein Glycoprotein


Mass: 28267.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus lujoense / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: C5ILC1
#3: Protein Glycoprotein


Mass: 6501.998 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus lujoense / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: C5ILC1

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Sugars , 4 types, 30 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spike complex from the Lujo virus / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Lujo mammarenavirus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87868 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002410164
ELECTRON MICROSCOPYf_angle_d0.540613722
ELECTRON MICROSCOPYf_chiral_restr0.03951758
ELECTRON MICROSCOPYf_plane_restr0.00321617
ELECTRON MICROSCOPYf_dihedral_angle_d5.75272184
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints4.25153988538E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints3.13706252216E-11
ens_2d_2GSCELECTRON MICROSCOPYNCS constraints1.10920614427E-10
ens_2d_3GSCELECTRON MICROSCOPYNCS constraints1.07828070919E-13
ens_3d_2BaELECTRON MICROSCOPYNCS constraints3.07173037023E-13
ens_3d_3BaELECTRON MICROSCOPYNCS constraints3.98113457944E-11

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