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- PDB-7qu2: Junin virus GP1 glycoprotein in complex with Fab fragment of anti... -

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Basic information

Entry
Database: PDB / ID: 7qu2
TitleJunin virus GP1 glycoprotein in complex with Fab fragment of antibody JUN1
Components
  • Fab JUN1 heavy chain
  • Fab JUN1 light chain
  • Glycoprotein G1
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)
Argentinian mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 JUN1 heavy chain
B: Fab JUN1 light chain
C: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2717
Polymers68,4423
Non-polymers8304
Water66737
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)69.847, 66.752, 73.101
Angle α, β, γ (deg.)90.000, 103.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Glycoprotein G1 / GP1


Mass: 18095.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argentinian mammarenavirus / Gene: GPC / Production host: Homo sapiens (human) / References: UniProt: C1K9J9

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Antibody , 2 types, 2 molecules AB

#1: Antibody Fab 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)
#2: Antibody Fab 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 , 2 types, 2 molecules

#4: 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-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: 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.: 1 / 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, 39 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% w/v PEG8000 and 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→67.92 Å / Num. obs: 22859 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.385 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.794 / Num. unique obs: 1100 / CC1/2: 0.742 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUZ

5nuz


Resolution: 2.5→67.92 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 1179 5.17 %
Rwork0.223 21619 -
obs0.2247 22798 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.47 Å2 / Biso mean: 75.0604 Å2 / Biso min: 40.76 Å2
Refinement stepCycle: final / Resolution: 2.5→67.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 54 37 4655
Biso mean--93.71 69.72 -
Num. residues----586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.610.42861470.40752654280198
2.61-2.750.37521500.356526392789100
2.75-2.920.34331580.318627192877100
2.92-3.150.39351400.288626782818100
3.15-3.460.28671420.242426952837100
3.46-3.960.24861190.219327492868100
3.96-4.990.19461480.167427312879100
4.99-67.920.20531750.181227542929100
Refinement TLS params.Method: refined / Origin x: 14.1813 Å / Origin y: -0.8831 Å / Origin z: 22.3838 Å
111213212223313233
T0.4331 Å20.0051 Å2-0.0456 Å2-0.6107 Å2-0.0717 Å2--0.3568 Å2
L2.9854 °21.6683 °2-1.8219 °2-1.5451 °2-1.2271 °2--1.8963 °2
S-0.0929 Å °-0.0823 Å °0.0518 Å °-0.1407 Å °0.0604 Å °0.0616 Å °-0.0263 Å °0.0833 Å °0.0326 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 215
2X-RAY DIFFRACTION1allB0 - 213
3X-RAY DIFFRACTION1allC87 - 230
4X-RAY DIFFRACTION1allC231 - 232
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allE1 - 37

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