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

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Basic information

Entry
Database: PDB / ID: 9ghj
TitleJunin virus GP1-GP2 heterodimer in complex with Fab of JUN1
Components
  • Glycoprotein G2
  • JUN1 heavy chain
  • JUN1 light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Junin virus glycoprotein prefusion Fab
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
TRIETHYLENE GLYCOL / Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus juninense
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBowden, T.A. / Paesen, G.C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
CitationJournal: To Be Published
Title: Structure and stabilization of the antigenic glycoprotein building blocks of the New World mammarenavirus spike complex.
Authors: Paesen, G.C. / Ng, W.M. / Sutton, G. / Doores, K.J. / Bowden, T.A.
History
DepositionAug 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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: Glycoprotein G2
H: JUN1 heavy chain
L: JUN1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,72310
Polymers95,6724
Non-polymers3,0516
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint2 kcal/mol
Surface area34840 Å2
Unit cell
Length a, b, c (Å)225.789, 71.974, 80.231
Angle α, β, γ (deg.)90.000, 95.895, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 22401.650 Da / Num. of mol.: 1 / Mutation: L88C, S249R, L250R, K251R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC / Production host: Spodoptera (butterflies/moths) / References: UniProt: C1K9J9
#2: Protein Glycoprotein G2 / GP2


Mass: 22924.672 Da / Num. of mol.: 1 / Mutation: E321P, M329C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC, GP-C / Production host: Spodoptera (butterflies/moths) / References: UniProt: P26313

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Antibody , 2 types, 2 molecules HL

#3: Antibody JUN1 heavy chain


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)
#4: Antibody JUN1 light chain


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)

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Sugars , 4 types, 5 molecules

#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+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.: 2
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

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Non-polymers , 2 types, 179 molecules

#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 293.65 K / Method: vapor diffusion, sitting drop
Details: 20% v/v 2-Propanol, 0.1 M Tris pH 8.0, 5% w/v PEG 8,000, 6% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→112.3 Å / Num. obs: 76048 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.6
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 3801 / CC1/2: 0.318

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→79.81 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 3680 4.9 %
Rwork0.2123 71430 -
obs0.214 75110 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.98 Å2
Refinement stepCycle: LAST / Resolution: 2.09→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 203 178 6363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026335
X-RAY DIFFRACTIONf_angle_d0.55538599
X-RAY DIFFRACTIONf_chiral_restr0.0415996
X-RAY DIFFRACTIONf_plane_restr0.00351062
X-RAY DIFFRACTIONf_dihedral_angle_d12.4262476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.39341430.39822522X-RAY DIFFRACTION90.4
2.12-2.150.42741330.37432579X-RAY DIFFRACTION94
2.15-2.180.32381240.35442634X-RAY DIFFRACTION94.81
2.18-2.210.35871210.34662651X-RAY DIFFRACTION95.69
2.21-2.240.35211460.32892665X-RAY DIFFRACTION96.37
2.24-2.280.35491410.31092709X-RAY DIFFRACTION98.45
2.28-2.320.35811350.31382790X-RAY DIFFRACTION99.59
2.32-2.360.32811430.30652732X-RAY DIFFRACTION99.76
2.36-2.410.34881330.31492769X-RAY DIFFRACTION99.9
2.41-2.460.33961600.28982740X-RAY DIFFRACTION99.97
2.46-2.510.32331480.26692796X-RAY DIFFRACTION99.93
2.51-2.570.2911570.24682752X-RAY DIFFRACTION99.76
2.57-2.630.22821350.22982752X-RAY DIFFRACTION99.83
2.63-2.70.27131220.21542786X-RAY DIFFRACTION99.9
2.7-2.780.26361410.20932782X-RAY DIFFRACTION99.97
2.78-2.870.2661420.22032782X-RAY DIFFRACTION100
2.87-2.980.28681570.24522756X-RAY DIFFRACTION100
2.98-3.10.29641480.22942772X-RAY DIFFRACTION100
3.1-3.240.27221330.21832767X-RAY DIFFRACTION100
3.24-3.410.21631520.20312798X-RAY DIFFRACTION100
3.41-3.620.1981290.19892796X-RAY DIFFRACTION100
3.62-3.90.21421470.18212782X-RAY DIFFRACTION100
3.9-4.290.18821400.16172811X-RAY DIFFRACTION100
4.29-4.910.18231510.14582799X-RAY DIFFRACTION100
4.91-6.190.21041380.17752835X-RAY DIFFRACTION100
6.19-79.810.24811610.20342873X-RAY DIFFRACTION99.57

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