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- PDB-7qu1: Machupo virus GP1 glycoprotein in complex with Fab fragment of an... -

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Basic information

Entry
Database: PDB / ID: 7qu1
TitleMachupo virus GP1 glycoprotein in complex with Fab fragment of antibody MAC1
Components
  • Fab MAC1 heavy chain
  • Fab MAC1 light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsIMMUNE SYSTEM / Arenavirus / Glycoprotein / Monoclonal Antibody / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Machupo mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsNg, W.M. / Sahin, M. / Krumm, S.A. / Seow, J. / Zeltina, A. / Harlos, K. / Paesen, G. / Pinschewer, D.D. / Doores, K.J. / Bowden, T.A.
Funding support United Kingdom, 8items
OrganizationGrant numberCountry
Wellcome Trust203797/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N002091/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K024426/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Swiss National Science Foundation310030_173132/1 United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V031635/1 United Kingdom
CitationJournal: Mbio / Year: 2022
Title: Contrasting Modes of New World Arenavirus Neutralization by Immunization-Elicited Monoclonal Antibodies.
Authors: Ng, W.M. / Sahin, M. / Krumm, S.A. / Seow, J. / Zeltina, A. / Harlos, K. / Paesen, G.C. / Pinschewer, D.D. / Doores, K.J. / Bowden, T.A.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab MAC1 heavy chain
B: Fab MAC1 light chain
C: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,52017
Polymers70,3763
Non-polymers3,14414
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.692, 100.731, 164.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 21050.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Machupo mammarenavirus / Gene: GPC, AVI34_00004 / Production host: Homo sapiens (human) / References: UniProt: Q6PXP4

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Antibody , 2 types, 2 molecules AB

#1: Antibody Fab MAC1 heavy chain


Mass: 25234.064 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)
#2: Antibody Fab 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 , 2 types, 4 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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.: 3 / 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 , 2 types, 368 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4 M sodium malonate (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→50.37 Å / Num. obs: 59374 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 35.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.3
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.515 / Num. unique obs: 2930 / CC1/2: 0.571 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
xia2data scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUZ

5nuz


Resolution: 1.91→50.37 Å / SU ML: 0.2714 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 3021 5.09 %
Rwork0.1944 56293 -
obs0.1962 59314 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.95 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 207 358 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00654892
X-RAY DIFFRACTIONf_angle_d0.81766623
X-RAY DIFFRACTIONf_chiral_restr0.0506755
X-RAY DIFFRACTIONf_plane_restr0.0072823
X-RAY DIFFRACTIONf_dihedral_angle_d11.60311817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.940.41171490.37092478X-RAY DIFFRACTION99.17
1.94-1.970.41151230.32752546X-RAY DIFFRACTION99.85
1.97-2.010.31851230.29912540X-RAY DIFFRACTION99.74
2.01-2.040.30441510.27792491X-RAY DIFFRACTION99.92
2.04-2.080.30691300.2612555X-RAY DIFFRACTION99.85
2.08-2.120.27551390.24552531X-RAY DIFFRACTION99.89
2.12-2.170.27991360.24582543X-RAY DIFFRACTION99.96
2.17-2.220.29951380.23592534X-RAY DIFFRACTION99.89
2.22-2.280.26331340.22512548X-RAY DIFFRACTION99.85
2.28-2.340.2711200.22972550X-RAY DIFFRACTION99.85
2.34-2.410.25141370.24212539X-RAY DIFFRACTION99.74
2.41-2.480.29331470.23882547X-RAY DIFFRACTION99.89
2.48-2.570.31491430.23562521X-RAY DIFFRACTION99.92
2.57-2.680.2311360.22362574X-RAY DIFFRACTION99.93
2.68-2.80.25951580.20462533X-RAY DIFFRACTION100
2.8-2.950.23851170.20512579X-RAY DIFFRACTION99.96
2.95-3.130.25111460.20522563X-RAY DIFFRACTION99.93
3.13-3.370.19921320.18692586X-RAY DIFFRACTION99.96
3.37-3.710.20111270.16092589X-RAY DIFFRACTION99.96
3.71-4.250.20451430.15372598X-RAY DIFFRACTION100
4.25-5.350.14091480.13612617X-RAY DIFFRACTION100
5.35-50.370.22731440.18762731X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 17.2064952757 Å / Origin y: 49.6124351035 Å / Origin z: 57.4155423281 Å
111213212223313233
T0.318428398446 Å20.0274572635407 Å20.0376011303572 Å2-0.340306285957 Å2-0.0597945733625 Å2--0.215590385908 Å2
L0.738039007951 °20.456011024711 °20.411080985817 °2-0.721736894649 °20.467093966656 °2--0.844622893276 °2
S-0.00824984649735 Å °0.00786913983631 Å °0.0901137855677 Å °0.0712797067523 Å °-0.100722542283 Å °0.148266510677 Å °0.0301127160217 Å °-0.100026839468 Å °0.11690382038 Å °
Refinement TLS groupSelection details: all

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