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- PDB-9ghi: Machupo virus GP1-GP2 heterodimer in complex with Fab of MAC1 -

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Basic information

Entry
Database: PDB / ID: 9ghi
TitleMachupo virus GP1-GP2 heterodimer in complex with Fab of MAC1
Components
  • Glycoprotein G2
  • MAC1 heavy chain
  • MAC1 light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Machupo 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
Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus machupoense
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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: 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
DepositionAug 15, 2024Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
B: Glycoprotein G2
H: MAC1 heavy chain
L: MAC1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,53011
Polymers96,0084
Non-polymers3,5217
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint8 kcal/mol
Surface area36180 Å2
Unit cell
Length a, b, c (Å)46.682, 73.585, 184.958
Angle α, β, γ (deg.)90.000, 91.003, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
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: 23546.824 Da / Num. of mol.: 1 / Mutation: L88C, E258S, S260R, L261K, K262R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus machupoense / Gene: GPC / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q8AZ57
#2: Protein Glycoprotein G2 / GP2


Mass: 23122.908 Da / Num. of mol.: 1 / Mutation: A263S, E332P, L340C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus machupoense / Gene: GPC, GP-C / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q6IUF7

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Antibody , 2 types, 2 molecules HL

#3: Antibody MAC1 heavy chain


Mass: 25248.092 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 MAC1 light chain


Mass: 24090.553 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 , 5 types, 7 molecules

#5: 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
#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
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
#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 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.: 1
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
#9: 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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 115 molecules

#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 90 mM Li2SO4, 90 mM Na2SO4, 90 mM K2SO4 12.5 % w/v PEG 4000, 20% w/v 1,2,6-Hexanetriol 0.1 M Gly-Gly/AMPD pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.41→184.93 Å / Num. obs: 48718 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 53.84 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.5
Reflection shellResolution: 2.41→2.45 Å / Num. unique obs: 2434 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→47.25 Å / SU ML: 0.4234 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 2449 5.03 %
Rwork0.2302 46192 -
obs0.232 48641 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.74 Å2
Refinement stepCycle: LAST / Resolution: 2.41→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 233 115 6411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266452
X-RAY DIFFRACTIONf_angle_d0.53298749
X-RAY DIFFRACTIONf_chiral_restr0.04251012
X-RAY DIFFRACTIONf_plane_restr0.00381089
X-RAY DIFFRACTIONf_dihedral_angle_d15.17022568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.460.38361470.36182689X-RAY DIFFRACTION97.73
2.46-2.510.38651660.34972628X-RAY DIFFRACTION99.82
2.51-2.570.33271670.33862705X-RAY DIFFRACTION99.76
2.57-2.630.36561310.30942726X-RAY DIFFRACTION99.79
2.63-2.710.29811390.31062669X-RAY DIFFRACTION99.75
2.71-2.790.37141640.33062679X-RAY DIFFRACTION99.89
2.79-2.880.40731290.3212706X-RAY DIFFRACTION99.89
2.88-2.980.33171510.2922712X-RAY DIFFRACTION99.9
2.98-3.10.32511420.26432727X-RAY DIFFRACTION99.97
3.1-3.240.31921300.25472704X-RAY DIFFRACTION100
3.24-3.410.29441410.26162716X-RAY DIFFRACTION100
3.41-3.620.29661450.24932758X-RAY DIFFRACTION99.93
3.62-3.90.23821460.21742717X-RAY DIFFRACTION100
3.9-4.290.22861400.18282730X-RAY DIFFRACTION100
4.29-4.920.18241490.16012719X-RAY DIFFRACTION99.93
4.92-6.190.25361150.18572793X-RAY DIFFRACTION100
6.19-47.250.20741470.20242814X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: 5.98373355808 Å / Origin y: 15.7275172113 Å / Origin z: 37.6183773405 Å
111213212223313233
T0.585889813259 Å2-0.00141957382983 Å20.0269580402922 Å2-0.332882748711 Å20.0171229883541 Å2--0.493716628288 Å2
L0.267169262481 °2-0.0469184199738 °2-0.300044464529 °2-0.246233459946 °20.368326593892 °2--2.62570367454 °2
S-0.0595931038241 Å °-0.0442694637214 Å °0.0067280445766 Å °0.324565147531 Å °0.0472508134077 Å °-0.0147094021261 Å °0.181295259829 Å °-0.0346412405671 Å °0.00752382449488 Å °
Refinement TLS groupSelection details: all

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