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- PDB-5yy4: Crystal structure of the scFv antibody 4B08 with sulfated epitope... -

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Basic information

Entry
Database: PDB / ID: 5yy4
TitleCrystal structure of the scFv antibody 4B08 with sulfated epitope peptide
Components
  • C-C chemokine receptor type 5
  • 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 / chemokine receptor activity / signaling / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine binding / 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 / chemokine receptor activity / signaling / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine binding / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / calcium ion transport / chemotaxis / MAPK cascade / cell-cell signaling / actin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / G alpha (i) signalling events / cell surface receptor signaling pathway / endosome / immune response / G protein-coupled receptor signaling pathway / inflammatory response / external side of plasma membrane / apoptotic process / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Chemokine receptor family / : / 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) / Immunoglobulins / Immunoglobulin-like ...CC chemokine receptor 5 / Chemokine receptor family / : / 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) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-C chemokine receptor type 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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: Biochemistry / Year: 2018
Title: Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody
Authors: Miyanabe, K. / Yamashita, T. / Abe, Y. / Akiba, H. / Takamatsu, Y. / Nakakido, M. / Hamakubo, T. / Ueda, T. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionDec 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / 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_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv 4B08
B: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3955
Polymers28,1672
Non-polymers2283
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.250, 56.610, 97.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFv 4B08


Mass: 26905.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PRA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3
#2: Protein/peptide C-C chemokine receptor type 5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 1261.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100mM sodium acetate, 1.4M Ammonium sulfate, pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→26.47 Å / Num. obs: 32983 / % possible obs: 95.6 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Net I/σ(I): 18.4
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1456 / CC1/2: 0.805 / Rpim(I) all: 0.279 / Rrim(I) all: 0.878 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLM7.2.1data reduction
Aimless7.0.046data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YD3

5yd3


Resolution: 1.59→26.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.568 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19443 1007 3.1 %RANDOM
Rwork0.15721 ---
obs0.15838 31928 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.59→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 11 266 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022048
X-RAY DIFFRACTIONr_bond_other_d0.0020.021788
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9652804
X-RAY DIFFRACTIONr_angle_other_deg0.95334183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90323.21887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6131513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
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_it1.291.811007
X-RAY DIFFRACTIONr_mcbond_other1.291.811006
X-RAY DIFFRACTIONr_mcangle_it1.9672.7061262
X-RAY DIFFRACTIONr_mcangle_other1.9672.7061263
X-RAY DIFFRACTIONr_scbond_it2.2052.0811041
X-RAY DIFFRACTIONr_scbond_other2.1792.0671033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.563.0161513
X-RAY DIFFRACTIONr_long_range_B_refined5.28621.6482271
X-RAY DIFFRACTIONr_long_range_B_other5.14820.9822210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 70 -
Rwork0.227 2116 -
obs--86.78 %

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