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- PDB-9mew: JUNV GP1, GP2, SSP and CR1-28 Fab complex in a pseudotyped virus ... -

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Basic information

Entry
Database: PDB / ID: 9mew
TitleJUNV GP1, GP2, SSP and CR1-28 Fab complex in a pseudotyped virus membrane
Components
  • CR1-28 Fab Heavy Chain
  • CR1-28 Fab Light Chain
  • JUNV GP1
  • JUNV GP2
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Viral protein / Glycoprotein / GPC / JUNV / Junin mammarenavirus / GP1 / GP2 / signal peptide / virus membrane / CR1-28 Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
MYRISTIC ACID / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus juninense
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTaylor, L.J. / Sawaya, M.R. / Castells-Graells, R. / Rodriguez, J.A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM145388 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128867 United States
Howard Hughes Medical Institute (HHMI)HHMI EPI United States
Department of Defense (DOD, United States)FA9550-23-1-0281 United States
CitationJournal: Cell Rep / Year: 2025
Title: In situ insights into antibody-mediated neutralization of a pre-fusion Junin virus glycoprotein complex.
Authors: Lily J Taylor / Michael R Sawaya / Jonna B Westover / Chenyi Wang / Frederick Jimenez / Aldo J Muñoz / Julian Whitelegge / Brian B Gowen / Gustavo F Helguera / Roger Castells-Graells / Jose A Rodriguez /
Abstract: A transmembrane glycoprotein complex (GPC) decorates the Junin mammarenavirus (JUNV) that causes New World hemorrhagic fevers. We leveraged single-particle cryoelectron microscopy (cryo-EM) to image ...A transmembrane glycoprotein complex (GPC) decorates the Junin mammarenavirus (JUNV) that causes New World hemorrhagic fevers. We leveraged single-particle cryoelectron microscopy (cryo-EM) to image the full-length JUNV GPC directly on pseudotyped virus (PV) membranes and bound by two JUNV-neutralizing antibodies: Candid#1 vaccine-elicited CR1-28 and J199, a potent therapeutic against Argentine hemorrhagic fever (AHF). The 3.8 Å resolution in situ structures of the antibody-neutralized, 3-fold symmetric JUNV GPC reveal its ectodomain architecture, signal peptide-bound transmembrane region, zinc-binding luminal domain, and post-translational modifications. JUNV-GPC sequence variants highlight the functional importance of the signal peptide transmembrane helix register for virus infection and attenuating Candid#1-associated variants. Overlapping CR1-28 and J199 epitopes suggest a common receptor-blocking mechanism for JUNV neutralization, while a J199-induced, symmetric GPC reorientation may further drive its potent inhibition of JUNV lethality in mice, compared to receptor blockade alone. This underscores the utility of in situ insights into GPC function and neutralization.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
B: JUNV GP1
C: JUNV GP2
D: CR1-28 Fab Light Chain
E: CR1-28 Fab Heavy Chain
F: Pre-glycoprotein polyprotein GP complex
G: JUNV GP1
H: JUNV GP2
I: CR1-28 Fab Light Chain
J: CR1-28 Fab Heavy Chain
K: Pre-glycoprotein polyprotein GP complex
L: JUNV GP1
M: JUNV GP2
N: CR1-28 Fab Light Chain
O: CR1-28 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,02739
Polymers307,50415
Non-polymers7,52224
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 "K"
d_2ens_1chain "F"
d_3ens_1chain "A"
d_1ens_2chain "G"
d_2ens_2chain "B"
d_3ens_2chain "L"
d_1ens_3chain "M"
d_2ens_3chain "C"
d_3ens_3chain "H"
d_1ens_4chain "I"
d_2ens_4chain "D"
d_3ens_4chain "N"
d_1ens_5chain "E"
d_2ens_5chain "J"
d_3ens_5chain "O"

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_1MYRMYRMYRMYRKHA101
d_12ens_1GLYGLYTHRTHRKK2 - 582 - 58
d_21ens_1MYRMYRMYRMYRFBA101
d_22ens_1GLYGLYTHRTHRFF2 - 582 - 58
d_31ens_1MYRMYRMYRMYRAV101
d_32ens_1GLYGLYTHRTHRAA2 - 582 - 58
d_11ens_2ALAALAARGARGGG61 - 2473 - 189
d_12ens_2NAGNAGNAGNAGGCA301
d_13ens_2NAGNAGNAGNAGGDA302
d_14ens_2NAGNAGNAGNAGRR1
d_15ens_2NAGNAGNAGNAGRR2
d_16ens_2BMABMABMABMARR3
d_21ens_2ALAALAARGARGBB61 - 2473 - 189
d_22ens_2NAGNAGNAGNAGBW301
d_23ens_2NAGNAGNAGNAGBX302
d_24ens_2NAGNAGNAGNAGPP1
d_25ens_2NAGNAGNAGNAGPP2
d_26ens_2BMABMABMABMAPP3
d_31ens_2ALAALAARGARGLL61 - 2473 - 189
d_32ens_2NAGNAGNAGNAGLIA301
d_33ens_2NAGNAGNAGNAGLJA302
d_34ens_2NAGNAGNAGNAGTT1
d_35ens_2NAGNAGNAGNAGTT2
d_36ens_2BMABMABMABMATT3
d_11ens_3ALAALAHISHISMM252 - 4851 - 234
d_12ens_3NAGNAGNAGNAGMKA501
d_13ens_3NAGNAGNAGNAGMLA502
d_14ens_3NAGNAGNAGNAGMMA503
d_15ens_3NAGNAGNAGNAGUU1
d_16ens_3NAGNAGNAGNAGUU2
d_17ens_3BMABMABMABMAUU3
d_21ens_3ALAALAHISHISCC252 - 4851 - 234
d_22ens_3NAGNAGNAGNAGCY501
d_23ens_3NAGNAGNAGNAGCZ502
d_24ens_3NAGNAGNAGNAGCAA503
d_25ens_3NAGNAGNAGNAGQQ1
d_26ens_3NAGNAGNAGNAGQQ2
d_27ens_3BMABMABMABMAQQ3
d_31ens_3ALAALAHISHISHH252 - 4851 - 234
d_32ens_3NAGNAGNAGNAGHEA501
d_33ens_3NAGNAGNAGNAGHFA502
d_34ens_3NAGNAGNAGNAGHGA503
d_35ens_3NAGNAGNAGNAGSS1
d_36ens_3NAGNAGNAGNAGSS2
d_37ens_3BMABMABMABMASS3
d_11ens_4ILEILEGLYGLYII2 - 2071 - 206
d_21ens_4ILEILEGLYGLYDD2 - 2071 - 206
d_31ens_4ILEILEGLYGLYNN2 - 2071 - 206
d_11ens_5GLNGLNPROPROEE1 - 2261 - 226
d_21ens_5GLNGLNPROPROJJ1 - 2261 - 226
d_31ens_5GLNGLNPROPROOO1 - 2261 - 226

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.499758215121, 0.866164953354, 9.92670935212E-7), (-0.866164953352, -0.499758215122, 1.72420084882E-6), (1.98953780258E-6, 1.86676442657E-9, 0.999999999998)112.931409849, 421.701757523, -0.000373308656805
2given(-0.500121909625, -0.865955007788, 3.12692865459E-7), (0.865955007787, -0.500121909625, -1.50765404494E-6), (1.46194512323E-6, -4.83232867266E-7, 0.999999999999)421.72950202, 113.034252687, -0.000194607530261
3given(-0.500119001395, 0.865956687394, 1.33371783891E-7), (-0.865956687394, -0.500119001395, 1.53261163113E-7), (1.9941929249E-7, -3.88453683216E-8, 1)113.033054073, 421.729313411, -3.25503621923E-5
4given(-0.499760879169, -0.866163416251, -4.60188467014E-7), (0.866163416251, -0.499760879169, -4.64568000911E-7), (1.72407613892E-7, -6.30771327277E-7, 1)421.702421258, 112.932507997, 7.20239700343E-5
5given(-0.500120167858, -0.865956013722, -1.18560067692E-8), (0.865956013722, -0.500120167858, -4.86474304335E-7), (4.15335921264E-7, -2.53562391103E-7, 1)421.729423284, 113.033535626, -2.83897910549E-5
6given(-0.499760013034, 0.866163915995, 7.36113124598E-7), (-0.866163915995, -0.499760013035, 4.29682085996E-7), (7.40055022984E-7, -4.22856701719E-7, 1)112.93200825, 421.702189277, -5.59545777605E-5
7given(-0.500119459662, 0.86595642273, 2.58771116185E-7), (-0.86595642273, -0.500119459662, 3.44743475584E-7), (4.27949297679E-7, -5.16715893472E-8, 1)113.033182339, 421.729341248, -8.90632567945E-5
8given(-0.499761132, -0.866163270372, 5.10050796321E-7), (0.866163270372, -0.499761132, -6.63714144353E-8), (3.12392044733E-7, 4.08617412587E-7, 1)421.702334592, 112.93249257, -0.000142390958047
9given(-0.500118854598, -0.865956772175, -1.435338619E-7), (0.865956772175, -0.500118854598, -2.13235212528E-7), (1.12868485745E-7, -2.30937069998E-7, 1)421.729363477, 113.033103061, 1.95127003764E-5
10given(-0.500119182563, 0.865956582764, -8.64173417245E-7), (-0.865956582764, -0.500119182563, -4.59461630121E-7), (-8.30063526156E-7, 5.18551084438E-7, 1)113.033276614, 421.729409316, 3.53739382177E-5

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Components

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Protein , 3 types, 9 molecules AFKBGLCHM

#1: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 6373.612 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC, GP-C / Cell line (production host): HEK293TT / Production host: Homo sapiens (human) / References: UniProt: P26313
#2: Protein JUNV GP1 / Pre-GP-C


Mass: 22311.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC, GP-C / Cell line (production host): HEK293TT / Production host: Homo sapiens (human) / References: UniProt: P26313
#3: Protein JUNV GP2 / Pre-GP-C


Mass: 27026.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC, GP-C / Cell line (production host): HEK293TT / Production host: Homo sapiens (human) / References: UniProt: P26313

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Antibody , 2 types, 6 molecules DINEJO

#4: Antibody CR1-28 Fab Light Chain


Mass: 22621.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293TT / Production host: Homo sapiens (human)
#5: Antibody CR1-28 Fab Heavy Chain


Mass: 24168.881 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293TT / Production host: Homo sapiens (human)

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Sugars , 2 types, 21 molecules

#6: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: 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.: 15 / 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, 3 molecules

#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has ligand of interestN
Has protein modificationY

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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: JUNV GP1, GP2, SSP and CR1-28 Fab complex in a virus membrane
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mammarenavirus juninense2169991
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397489 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002522284
ELECTRON MICROSCOPYf_angle_d0.546530234
ELECTRON MICROSCOPYf_chiral_restr0.04443435
ELECTRON MICROSCOPYf_plane_restr0.0043777
ELECTRON MICROSCOPYf_dihedral_angle_d13.48988523
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2HAKELECTRON MICROSCOPYNCS constraints3.4754337281E-13
ens_1d_3HAKELECTRON MICROSCOPYNCS constraints2.74834519194E-13
ens_2d_2GGELECTRON MICROSCOPYNCS constraints1.96429271275E-12
ens_2d_3GGELECTRON MICROSCOPYNCS constraints4.57754077459E-13
ens_3d_2MMELECTRON MICROSCOPYNCS constraints1.76716624127E-11
ens_3d_3MMELECTRON MICROSCOPYNCS constraints4.3032316148E-13
ens_4d_2IIELECTRON MICROSCOPYNCS constraints3.22251755529E-12
ens_4d_3IIELECTRON MICROSCOPYNCS constraints1.00937927373E-12
ens_5d_2EEELECTRON MICROSCOPYNCS constraints3.43103169573E-13
ens_5d_3EEELECTRON MICROSCOPYNCS constraints5.97713881152E-13

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