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- PDB-5yd4: Crystal structure of the scFv antibody 4B08 with epitope peptide ... -

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Basic information

Entry
Database: PDB / ID: 5yd4
TitleCrystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)
Components
  • Epitope peptide (mutation T6A)
  • 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 / immunoglobulin complex / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / antigen binding / coreceptor activity / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / cell-cell signaling / actin binding / virus receptor activity / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / adaptive immune response / 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 / : / : / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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: 1.35 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv 4B08
B: Epitope peptide (mutation T6A)
C: scFv 4B08
D: Epitope peptide (mutation T6A)
E: scFv 4B08
F: Epitope peptide (mutation T6A)
G: scFv 4B08
H: Epitope peptide (mutation T6A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,04716
Polymers111,2798
Non-polymers7698
Water16,538918
1
A: scFv 4B08
B: Epitope peptide (mutation T6A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0124
Polymers27,8202
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-35 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: scFv 4B08
D: Epitope peptide (mutation T6A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1085
Polymers27,8202
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-31 kcal/mol
Surface area10700 Å2
MethodPISA
3
E: scFv 4B08
F: Epitope peptide (mutation T6A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1085
Polymers27,8202
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-27 kcal/mol
Surface area11110 Å2
MethodPISA
4
G: scFv 4B08
H: Epitope peptide (mutation T6A)


Theoretical massNumber of molelcules
Total (without water)27,8202
Polymers27,8202
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-17 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.470, 72.900, 86.460
Angle α, β, γ (deg.)90.00, 114.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
scFv 4B08


Mass: 26748.613 Da / Num. of mol.: 4
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
Epitope peptide (mutation T6A)


Mass: 1071.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 918 / 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 or E + F or G + H
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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: 1.35→33.1 Å / Num. obs: 197862 / % possible obs: 99.1 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.44 / Net I/σ(I): 10.6
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 27517 / CC1/2: 0.843 / Rpim(I) all: 0.238 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YD3

5yd3


Resolution: 1.35→33.1 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.743 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17338 3797 1.9 %RANDOM
Rwork0.1354 ---
obs0.13612 194038 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.06 Å2
2--0.04 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.35→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7394 0 40 918 8352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027869
X-RAY DIFFRACTIONr_bond_other_d0.0010.027080
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.94810726
X-RAY DIFFRACTIONr_angle_other_deg0.875316372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64351009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21423.14344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.763151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5621547
X-RAY DIFFRACTIONr_chiral_restr0.1160.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028993
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021914
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_it2.6691.5173867
X-RAY DIFFRACTIONr_mcbond_other2.6681.5173866
X-RAY DIFFRACTIONr_mcangle_it3.0342.2764834
X-RAY DIFFRACTIONr_mcangle_other3.0332.2784835
X-RAY DIFFRACTIONr_scbond_it3.1451.8024002
X-RAY DIFFRACTIONr_scbond_other3.1041.7923970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5362.5845810
X-RAY DIFFRACTIONr_long_range_B_refined4.01813.789445
X-RAY DIFFRACTIONr_long_range_B_other3.83113.2178989
X-RAY DIFFRACTIONr_rigid_bond_restr6.277314949
X-RAY DIFFRACTIONr_sphericity_free23.3795291
X-RAY DIFFRACTIONr_sphericity_bonded9.651515383
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 227 -
Rwork0.185 13107 -
obs--90.78 %

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