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- PDB-9qqn: Junin virus GP1-GP2 heterodimer in complex with Fab of JUN1 -

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Basic information

Entry
Database: PDB / ID: 9qqn
TitleJunin virus GP1-GP2 heterodimer in complex with Fab of JUN1
Components
  • Chains: C
  • Chains: D
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Junin virus / glycoprotein / stabilized protomer
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
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus juninense
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBowden, T.A. / Paesen, G.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Mbio / Year: 2025
Title: Structure and stabilization of the antigenic glycoprotein building blocks of the New World mammarenavirus spike complex.
Authors: Paesen, G.C. / Ng, W.M. / Kimuda, S. / Sutton, G. / Doores, K.J. / Bowden, T.A.
History
DepositionApr 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 16, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
B: Pre-glycoprotein polyprotein GP complex
C: Chains: C
D: Chains: D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,1539
Polymers153,7664
Non-polymers3,3875
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint5 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.468, 73.030, 80.734
Angle α, β, γ (deg.)90.000, 95.777, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules CD

#2: Antibody Chains: C


Mass: 23943.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Chains: D


Mass: 26402.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 177 molecules AB

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


Mass: 51709.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C1K9J9
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 5 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.5 mM Yttrium(III) chloride hexahydrate, 0.5 mM Erbium(III) chloride hexahydrate, 0.5 mM Terbium(III) chloride hexahydrate, 0.5 mM Ytterbium(III) chloride hexahydrate 0.1 M MOPSO/Bis-Tris, ...Details: 0.5 mM Yttrium(III) chloride hexahydrate, 0.5 mM Erbium(III) chloride hexahydrate, 0.5 mM Terbium(III) chloride hexahydrate, 0.5 mM Ytterbium(III) chloride hexahydrate 0.1 M MOPSO/Bis-Tris, pH 6.5 10% w/v PEG 8000, 20% v/v 1,5-Pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.55→112.66 Å / Num. obs: 43012 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 62.39 Å2 / CC1/2: 1 / Net I/σ(I): 7.2
Reflection shellResolution: 2.55→2.59 Å / Num. unique obs: 2206 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→80.32 Å / SU ML: 0.396 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 2082 4.87 %
Rwork0.2011 40685 -
obs0.2029 42767 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.07 Å2
Refinement stepCycle: LAST / Resolution: 2.55→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 226 175 6406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266383
X-RAY DIFFRACTIONf_angle_d0.58378668
X-RAY DIFFRACTIONf_chiral_restr0.0411014
X-RAY DIFFRACTIONf_plane_restr0.00451065
X-RAY DIFFRACTIONf_dihedral_angle_d16.50452496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.41051320.35762613X-RAY DIFFRACTION95.21
2.61-2.670.41811590.33892603X-RAY DIFFRACTION97.74
2.68-2.750.30831440.30922669X-RAY DIFFRACTION99.12
2.75-2.830.34311400.29112724X-RAY DIFFRACTION99.76
2.83-2.920.34791440.27342716X-RAY DIFFRACTION99.93
2.92-3.020.34771330.26672705X-RAY DIFFRACTION99.89
3.02-3.140.28671340.23222710X-RAY DIFFRACTION99.96
3.14-3.290.27091290.22142742X-RAY DIFFRACTION99.97
3.29-3.460.25911150.21012715X-RAY DIFFRACTION99.82
3.46-3.680.26871410.21142747X-RAY DIFFRACTION99.93
3.68-3.960.21171330.18442712X-RAY DIFFRACTION99.86
3.96-4.360.19191500.16882743X-RAY DIFFRACTION99.86
4.36-4.990.18621430.1492725X-RAY DIFFRACTION99.69
4.99-6.290.18981500.17592747X-RAY DIFFRACTION99.76
6.29-80.320.21111350.18252814X-RAY DIFFRACTION99.03

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