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- PDB-7nw3: X-ray crystallographic study of PIYDIN, which contains the trunca... -

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Basic information

Entry
Database: PDB / ID: 7nw3
TitleX-ray crystallographic study of PIYDIN, which contains the truncation determinants of binding PI and N, bound to RoAb13, a CCR5 antibody
Components
  • Antibody RoAb13 Heavy Chain
  • Antibody RoAb13 Light Chain
  • Region from C-C chemokine receptor type 5 N-terminal domain
KeywordsIMMUNE SYSTEM / immunoglobulin / anti-CCR5 antibody / epitope binding
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 / 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 / virus receptor activity / cell-cell signaling / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / 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)
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: 3.20001097294 Å
AuthorsSaridakis, E. / Helliwell, J.R. / Govada, L. / Chayen, N.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/K503733/1 United Kingdom
CitationJournal: Iucrj / Year: 2021
Title: X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5.
Authors: Govada, L. / Saridakis, E. / Kassen, S.C. / Bin-Ramzi, A. / Morgan, R.M. / Chain, B. / Helliwell, J.R. / Chayen, N.E.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
H: Antibody RoAb13 Heavy Chain
L: Antibody RoAb13 Light Chain
A: Region from C-C chemokine receptor type 5 N-terminal domain


Theoretical massNumber of molelcules
Total (without water)49,2573
Polymers49,2573
Non-polymers00
Water724
1
H: Antibody RoAb13 Heavy Chain
L: Antibody RoAb13 Light Chain

A: Region from C-C chemokine receptor type 5 N-terminal domain


Theoretical massNumber of molelcules
Total (without water)49,2573
Polymers49,2573
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
Buried area4300 Å2
ΔGint-27 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.607, 76.607, 270.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody Antibody RoAb13 Heavy Chain


Mass: 24063.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody RoAb13 Light Chain


Mass: 24459.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Region from C-C chemokine receptor type 5 N-terminal domain / / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor / PIYDIN


Mass: 733.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 10 mg/ml protein, 20 mM HEPES pH 7.0, 0.1 M sodium chloride, 660 uM PIYDIN peptide, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→270.06 Å / Num. obs: 14151 / % possible obs: 99.9 % / Redundancy: 24.8 % / Biso Wilson estimate: 135.11414236 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.037 / Rrim(I) all: 0.183 / Net I/σ(I): 14.3
Reflection shellResolution: 3.2→3.37 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1984 / CC1/2: 0.529 / Rpim(I) all: 1.228

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2S

4s2s


Resolution: 3.20001097294→67.515 Å / SU ML: 0.661375880758 / Cross valid method: FREE R-VALUE / σ(F): 1.34416359481 / Phase error: 40.2897604967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.292693257892 728 5.17449712133 %
Rwork0.268273678187 13341 -
obs0.269545672354 14069 99.8864039759 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 173.688789619 Å2
Refinement stepCycle: LAST / Resolution: 3.20001097294→67.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 4 3328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004013744925473407
X-RAY DIFFRACTIONf_angle_d0.79155708134638
X-RAY DIFFRACTIONf_chiral_restr0.0478509479134524
X-RAY DIFFRACTIONf_plane_restr0.0047339297548588
X-RAY DIFFRACTIONf_dihedral_angle_d3.15448089822380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.20001097294-3.44710.4840718340111450.4316017223312563X-RAY DIFFRACTION99.8157021747
3.4471-3.79390.3554642001111530.3496627058922594X-RAY DIFFRACTION99.7096188748
3.7939-4.34280.294521246051270.2604457252282650X-RAY DIFFRACTION99.9640028798
4.3428-5.47120.2353069821511370.2300275646332695X-RAY DIFFRACTION100
5.4712-67.5150.2862850579271660.2580257943322839X-RAY DIFFRACTION99.9334885268
Refinement TLS params.Method: refined / Origin x: 26.0172256866 Å / Origin y: 4.46033682254 Å / Origin z: 54.9396930983 Å
111213212223313233
T1.46384605942 Å2-0.26521892302 Å20.219325884159 Å2-1.09996574952 Å20.125407398143 Å2--1.10814943902 Å2
L3.01679991567 °20.357530399108 °2-2.48311301472 °2-0.947692380994 °2-1.03565169204 °2--2.93806333459 °2
S0.337118876336 Å °-1.02104733657 Å °-0.294121081666 Å °-0.207853781322 Å °-0.201499222825 Å °-0.0614286765302 Å °-0.431823455752 Å °0.887958933958 Å °-0.0155974305569 Å °
Refinement TLS groupSelection details: all

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