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

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Basic information

Entry
Database: PDB / ID: 9luy
TitleSingle-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog
ComponentsSingle-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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

Downloads & links

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Assembly

Deposited unit
A: Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2122
Polymers29,1201
Non-polymers921
Water3,765209
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)76.054, 71.390, 43.352
Angle α, β, γ (deg.)90.000, 100.908, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-492-

HOH

31A-593-

HOH

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Components

#1: Antibody Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog


Mass: 29120.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken chromosome 6 C10orf76 homolog (residues 3-22), a linker (residues 23-30), the light chain (residues ...Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken chromosome 6 C10orf76 homolog (residues 3-22), a linker (residues 23-30), the light chain (residues 31-140), a second linker (residues 141-155), and the heavy chain (residues 156-273).
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 6.5, 12% w/v polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 28848 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.29 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.4
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2 / Num. unique obs: 1429 / CC1/2: 0.656 / % possible all: 100

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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: 1.62→31.14 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1881 1441 5 %
Rwork0.1668 27392 -
obs0.1679 28833 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.66 Å2
Refinement stepCycle: LAST / Resolution: 1.62→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 6 209 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871932
X-RAY DIFFRACTIONf_angle_d1.05992619
X-RAY DIFFRACTIONf_chiral_restr0.0635284
X-RAY DIFFRACTIONf_plane_restr0.0067336
X-RAY DIFFRACTIONf_dihedral_angle_d14.1668708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.2691450.24332758X-RAY DIFFRACTION99.9
1.68-1.750.31221440.23222731X-RAY DIFFRACTION99.86
1.75-1.820.27221430.2222717X-RAY DIFFRACTION99.76
1.82-1.920.2381440.18242725X-RAY DIFFRACTION99.76
1.92-2.040.20691430.17542750X-RAY DIFFRACTION99.72
2.04-2.20.19471440.17292737X-RAY DIFFRACTION99.86
2.2-2.420.20591440.16012734X-RAY DIFFRACTION99.55
2.42-2.770.17751450.16992746X-RAY DIFFRACTION99.59
2.77-3.490.17171430.15542739X-RAY DIFFRACTION99.04
3.49-31.140.14811460.1442755X-RAY DIFFRACTION98.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.228090269910.0975193763184-1.303768918332.976064007130.5137194162923.200615912030.118874073069-0.1227544827710.07116249254750.0821802597166-0.05006497770020.1564944255550.003484928163860.0500130543511-0.04707917303190.0945094647638-0.0173274427468-0.01397612356730.08460326126350.00533191924190.13829684452215.2639168905-7.381273514073.60991164893
26.098043973582.371208324250.4517518051063.972521735930.0941411301312.41717616742-0.0513793686005-0.03042584523880.373484473736-0.111716395231-0.001004609463260.5981423408050.0315434965621-0.1597864195670.009990129958710.1166886187510.009788499197230.01500438693540.107608750302-0.05588346228350.2037925708778.29551357352-4.682981126966.20281644464
34.12084859116-2.47558461050.7703665792645.268971786381.982651303881.73026304299-0.03201999199690.0136815386295-0.161274301520.1499919201230.111877735662-0.290900449402-0.02910250037540.627679283673-0.01688639139370.129736529261-0.0134972690447-0.04549333454990.1997408764110.01685064065480.20450668127328.4130852576-3.793550412957.94903394994
41.83650153784-0.591560634397-0.3822150365223.58393852545-0.4950278397422.21050405135-0.0394282088273-0.136570910409-0.02067238986670.329157579771-0.03975631626760.037417222347-0.0547824770042-0.03417556297740.0658316255790.136640684164-0.0236716861659-0.01077690996070.144829993438-0.0340979231930.12524210713712.719434685813.682539368213.3808160634
51.258931696740.238023415173-0.06949150756871.101290470430.9044655784870.8778401492080.0793231929212-0.114700061002-0.04092787883570.177761782668-0.170231966580.2271774618280.042427598899-0.1186574821720.08470009118610.186811903504-0.0178523111930.0225916554430.1492219996720.0200371956510.2224211747614.07723864339-2.085450923439.11003816673
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 179 through 238 )179 - 238148 - 207
22chain 'A' and (resid 239 through 273 )239 - 273208 - 242
33chain 'A' and (resid 2 through 33 )2 - 331 - 19
44chain 'A' and (resid 34 through 124 )34 - 12420 - 110
55chain 'A' and (resid 125 through 178 )125 - 178111 - 147

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