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- PDB-8jow: Crystal structure of rabbit antibody with phosphorylated peptide bound -

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Basic information

Entry
Database: PDB / ID: 8jow
TitleCrystal structure of rabbit antibody with phosphorylated peptide bound
Components
  • ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER
  • Antibody (scFv)
KeywordsIMMUNE SYSTEM / Binding Rabbit antibody Phosphorylated serine Selectivity Post-translational modification Antibody Antigen
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCaaveiro, J.M.M. / Kawade, R. / Tsumoto, K.
Funding support Japan, 15items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H04202 Japan
Japan Society for the Promotion of Science (JSPS)JP16H02420 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05766 Japan
Japan Society for the Promotion of Science (JSPS)JP20H02531 Japan
Japan Agency for Medical Research and Development (AMED)JP20wm0325002s Japan
Japan Agency for Medical Research and Development (AMED)JP19ak0101117h Japan
Japan Agency for Medical Research and Development (AMED)JP20ak0101139h Japan
Japan Agency for Medical Research and Development (AMED)JP18ak0101100h Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101094j Japan
Japan Agency for Medical Research and Development (AMED)JP18dm0107064h Japan
Japan Agency for Medical Research and Development (AMED)JP18mk0101081h Japan
Japan Agency for Medical Research and Development (AMED)JP18fm0208030h Japan
Japan Agency for Medical Research and Development (AMED)JP18fk0108073h Japan
Japan Agency for Medical Research and Development (AMED)JP18ak0101100h Japan
Japan Science and TechnologyJPMJCR20H8 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies.
Authors: Kasahara, K. / Kawade, R. / Nakakido, M. / Matsunaga, R. / Akiba, H. / Entzminger, K.C. / Maruyama, T. / Okumura, S.C.J. / Caaveiro, J.M.M. / Kuroda, D. / Tsumoto, K.
History
DepositionJun 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 25, 2024Group: 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.journal_volume / _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: Antibody (scFv)
B: ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER
C: Antibody (scFv)
D: ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5936
Polymers53,5234
Non-polymers712
Water8,233457
1
A: Antibody (scFv)
B: ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8324
Polymers26,7612
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-17 kcal/mol
Surface area10450 Å2
MethodPISA
2
C: Antibody (scFv)
D: ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER


Theoretical massNumber of molelcules
Total (without water)26,7612
Polymers26,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-17 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.520, 43.560, 63.520
Angle α, β, γ (deg.)71.31, 84.39, 87.57
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Antibody (scFv)


Mass: 25255.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide ARG-PRO-HIS-PHE-PRO-GLN-PHE-SEP-TYR-SER-ALA-SER


Mass: 1505.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Lithium chloride, 20 % w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→41.3 Å / Num. obs: 77744 / % possible obs: 88.8 % / Redundancy: 1.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.7
Reflection shellResolution: 1.4→1.47 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10677 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.825 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2329 3 %RANDOM
Rwork0.16202 ---
obs0.16321 75415 88.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.213 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20.01 Å2-0.1 Å2
2---0.42 Å2-0.44 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.4→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 2 457 4016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0113706
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163336
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6495064
X-RAY DIFFRACTIONr_angle_other_deg0.5631.5597709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7755490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.965520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02810551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.1371918
X-RAY DIFFRACTIONr_mcbond_other0.8971.1371918
X-RAY DIFFRACTIONr_mcangle_it1.2182.0342389
X-RAY DIFFRACTIONr_mcangle_other1.2182.0352390
X-RAY DIFFRACTIONr_scbond_it0.9311.2671788
X-RAY DIFFRACTIONr_scbond_other0.9311.2671789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3152.2752665
X-RAY DIFFRACTIONr_long_range_B_refined2.07113.193992
X-RAY DIFFRACTIONr_long_range_B_other1.88212.033897
X-RAY DIFFRACTIONr_rigid_bond_restr3.44237042
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.431 Å
RfactorNum. reflection% reflection
Rfree0.292 140 -
Rwork0.248 4960 -
obs--78.85 %

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