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- PDB-9lux: Single-chain Fv antibody of G2 fused with antigen peptide from ch... -

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Basic information

Entry
Database: PDB / ID: 9lux
TitleSingle-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
ComponentsMajor prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Post-translational modification: synthesis of GPI-anchored proteins / basement membrane / synaptic cleft / side of membrane / protein homooligomerization / copper ion binding / plasma membrane
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Major prion protein homolog
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHanazono, Y. / Yabuno, S. / Hayashi, T. / Numoto, N. / Ito, N. / Oda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2025
Title: Crystal structures reveal how the multispecific antibody G2 achieves binding to different peptides.
Authors: Hanazono, Y. / Yabuno, S. / Hayashi, T. / Numoto, N. / Kamatari, Y.O. / Ito, N. / Oda, M.
History
DepositionFeb 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
B: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
C: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
D: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
E: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
F: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,65125
Polymers172,8426
Non-polymers1,80919
Water17,691982
1
A: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2836
Polymers28,8071
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0914
Polymers28,8071
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3757
Polymers28,8071
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0954
Polymers28,8071
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9032
Polymers28,8071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9032
Polymers28,8071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.360, 86.720, 86.580
Angle α, β, γ (deg.)105.127, 107.911, 100.880
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody
Major prion protein homolog,Single-chain Fv antibody of G2 fused with antigen peptide from chicken prion protein / 65-21 protein / Acetylcholine receptor-inducing activity / ARIA / PR-LP


Mass: 28806.979 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken prion protein (residues 3-20), a linker (residues 21-28), the light chain (residues 29-138), a second ...Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken prion protein (residues 3-20), a linker (residues 21-28), the light chain (residues 29-138), a second linker (residues 139-153), and the heavy chain (residues 154-271).
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Mus musculus (house mouse)
Gene: PRNP, PRN-P / Production host: Escherichia coli (E. coli) / References: UniProt: P27177
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / Source method: isolated from a natural source / Formula: H2O
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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M ammonium sulphate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 183582 / % possible obs: 97.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.5
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 29434 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PGX

6pgx


Resolution: 1.85→49.32 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.7367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 9155 4.99 %
Rwork0.1943 174403 -
obs0.1959 183558 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11622 0 99 982 12703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008511974
X-RAY DIFFRACTIONf_angle_d1.014216233
X-RAY DIFFRACTIONf_chiral_restr0.06011766
X-RAY DIFFRACTIONf_plane_restr0.00722091
X-RAY DIFFRACTIONf_dihedral_angle_d14.00874297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.33232870.30865771X-RAY DIFFRACTION97.22
1.87-1.890.34993260.29935870X-RAY DIFFRACTION98.19
1.89-1.920.3283080.29325906X-RAY DIFFRACTION98.29
1.92-1.940.2763010.27715806X-RAY DIFFRACTION98.45
1.94-1.970.31672860.26385942X-RAY DIFFRACTION98.47
1.97-1.990.28343330.25415809X-RAY DIFFRACTION98.29
1.99-2.020.27143220.24275895X-RAY DIFFRACTION98.45
2.02-2.050.27343110.24135864X-RAY DIFFRACTION98.16
2.05-2.080.27473100.23265780X-RAY DIFFRACTION98.19
2.08-2.120.26372800.23135997X-RAY DIFFRACTION98.28
2.12-2.150.25683290.23015826X-RAY DIFFRACTION98.21
2.15-2.190.27532920.21475785X-RAY DIFFRACTION98.08
2.19-2.240.24942880.21375898X-RAY DIFFRACTION97.93
2.24-2.280.25223280.21735802X-RAY DIFFRACTION97.74
2.28-2.330.26213040.21755834X-RAY DIFFRACTION97.31
2.33-2.390.26873180.21425760X-RAY DIFFRACTION97.53
2.39-2.440.26893180.2075780X-RAY DIFFRACTION96.96
2.44-2.510.27442700.20955790X-RAY DIFFRACTION96.53
2.51-2.580.26252950.21135288X-RAY DIFFRACTION89.51
2.58-2.670.27932720.22085709X-RAY DIFFRACTION95.09
2.67-2.760.2623240.22425895X-RAY DIFFRACTION98.59
2.76-2.870.25343070.21435908X-RAY DIFFRACTION98.62
2.87-30.22723130.20395865X-RAY DIFFRACTION98.66
3-3.160.22023000.19795884X-RAY DIFFRACTION98.53
3.16-3.360.22453150.19765875X-RAY DIFFRACTION98.36
3.36-3.620.20753110.17525856X-RAY DIFFRACTION98.04
3.62-3.990.20923170.1715798X-RAY DIFFRACTION97.86
3.99-4.560.17033050.14445787X-RAY DIFFRACTION96.47
4.56-5.750.15982920.15145487X-RAY DIFFRACTION92.2
5.75-49.320.20142930.17975936X-RAY DIFFRACTION99.36

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