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- PDB-5yd5: Crystal structure of the scFv antibody 4B08 with epitope peptide ... -

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Basic information

Entry
Database: PDB / ID: 5yd5
TitleCrystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)
Components
  • Peptide epitope (mutation N3A)
  • scFv 4B08
KeywordsIMMUNE SYSTEM / Antibody / Biomolecular recognition / MD simulations / Thermodynamics
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / immunoglobulin complex / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / antigen binding / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / adaptive immune response / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Chemokine receptor family / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) ...CC chemokine receptor 5 / Chemokine receptor family / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-II region 7S34.1 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsCaaveiro, J.M.M. / Miyanabe, K. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25249115 Japan
Japan Society for the Promotion of Science15K06962 Japan
CitationJournal: J. Biochem. / Year: 2018
Title: Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
Authors: Miyanabe, K. / Akiba, H. / Kuroda, D. / Nakakido, M. / Kusano-Arai, O. / Iwanari, H. / Hamakubo, T. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionSep 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
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_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv 4B08
B: Peptide epitope (mutation N3A)
C: scFv 4B08
D: Peptide epitope (mutation N3A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38212
Polymers55,6134
Non-polymers7698
Water6,467359
1
A: scFv 4B08
B: Peptide epitope (mutation N3A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2877
Polymers27,8072
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-52 kcal/mol
Surface area11310 Å2
MethodPISA
2
C: scFv 4B08
D: Peptide epitope (mutation N3A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0955
Polymers27,8072
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-51 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 81.900, 114.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Antibody scFv 4B08


Mass: 26748.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P01630*PLUS
#2: Protein/peptide Peptide epitope (mutation N3A)


Mass: 1058.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Compound detailsdimeric means one chain of antibody and one chain of peptide A + B or C + D

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM BIS-TRIS 1.8 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→37.3 Å / Num. obs: 40361 / % possible obs: 95.6 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.065 / Net I/σ(I): 10
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2555 / CC1/2: 0.939 / Rpim(I) all: 0.174 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YD3

5yd3


Resolution: 1.96→37.3 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.994 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 1584 3.9 %RANDOM
Rwork0.20342 ---
obs0.20548 38732 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.291 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å20 Å2
2--10 Å20 Å2
3----7.09 Å2
Refinement stepCycle: 1 / Resolution: 1.96→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 40 359 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194013
X-RAY DIFFRACTIONr_bond_other_d0.0020.023483
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9535448
X-RAY DIFFRACTIONr_angle_other_deg0.95138109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.59223.171164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08315617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5971521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
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_it1.1221.5592035
X-RAY DIFFRACTIONr_mcbond_other1.1211.5592034
X-RAY DIFFRACTIONr_mcangle_it1.8182.3272538
X-RAY DIFFRACTIONr_mcangle_other1.8182.3272539
X-RAY DIFFRACTIONr_scbond_it1.681.6781977
X-RAY DIFFRACTIONr_scbond_other1.5861.6421945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.522.3922856
X-RAY DIFFRACTIONr_long_range_B_refined4.28217.9074529
X-RAY DIFFRACTIONr_long_range_B_other4.15617.7294473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 104 -
Rwork0.235 2568 -
obs--86.5 %

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