[English] 日本語
Yorodumi
- PDB-8p4t: The spike complex of the Lujo Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p4t
TitleThe spike complex of the Lujo Virus
Components(Glycoprotein) x 3
KeywordsVIRAL PROTEIN / Spike complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / host cell Golgi apparatus / endocytosis involved in viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
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: Nat Commun / Year: 2024
Title: The structure of the Lujo virus spike complex.
Authors: Maayan Eilon-Ashkenazy / Hadas Cohen-Dvashi / Sarah Borni / Ron Shaked / Rivka Calinsky / Yaakov Levy / Ron Diskin /
Abstract: Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old ...Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old World" and "New World" serogroups, but it uses a cell-entry receptor, neuropilin-2 (NRP2), that is distinct from the receptors of OW and NW viruses. Though the receptor binding domain of LUJV has been characterized structurally, the overall organization of the trimeric spike complex and how NRP2 is recognized in this context were unknown. Here, we present the structure of the membrane-embedded LUJV spike complex determined by cryo-electron microscopy. Analysis of the structure suggested that a single NRP2 molecule is bound at the apex of the trimeric spike and that multiple subunits of the trimer contact the receptor. The binding of NRP2 involves an intriguing arginine-methionine interaction, which we analyzed using quantum mechanical modeling methods. We compare the LUJV spike structure with the only other available structure of a complete arenaviral spike, which is the Lassa virus. The similarities and differences between them shed light on Arenavirus evolution, inform vaccine design, and provide information that will be useful in combating future Arenavirus outbreaks.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more