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- PDB-7njz: X-ray crystallography study of RoAb13 which binds to PIYDIN, a pa... -

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Basic information

Entry
Database: PDB / ID: 7njz
TitleX-ray crystallography study of RoAb13 which binds to PIYDIN, a part of the CCR5 N terminal domain
Components
  • Antibody RoAb13 Heavy Chain
  • Antibody RoAb13 Light Chain
  • Region from C-C chemokine receptor type 5 N-terminal domain
KeywordsIMMUNE SYSTEM / CCR5 Peptidomimetic
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 / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / endosome / inflammatory response / immune 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: 3.2 Å
AuthorsHelliwell, J.R. / Chayen, N. / Saridakis, E. / Govada, L.
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
DepositionFeb 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,2573
Polymers49,2573
Non-polymers00
Water39622
1
H: Antibody RoAb13 Heavy Chain
L: Antibody RoAb13 Light Chain

C: 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 area4240 Å2
ΔGint-24 kcal/mol
Surface area20560 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-22 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.440, 76.440, 268.639
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.: 22 / 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: 3.88 Å3/Da / Density % sol: 68 % / Description: Bipyramidal.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.85 M Ammonium sulfate / PH range: 5.0 - 6.0
Temp details: All experiments were incubated in a temperature controlled Incubator at 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2→73.53 Å / Num. obs: 13940 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 121.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 3.2→3.5 Å / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2703 / CC1/2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2S

4s2s


Resolution: 3.2→73.52 Å / SU ML: 0.6142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.1435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2922 707 5.07 %
Rwork0.2692 13233 -
obs0.2703 13940 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.77 Å2
Refinement stepCycle: LAST / Resolution: 3.2→73.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 22 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343399
X-RAY DIFFRACTIONf_angle_d0.66044623
X-RAY DIFFRACTIONf_chiral_restr0.0445523
X-RAY DIFFRACTIONf_plane_restr0.01587
X-RAY DIFFRACTIONf_dihedral_angle_d7.2193473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.40811620.39612531X-RAY DIFFRACTION99.59
3.45-3.790.32191440.32712576X-RAY DIFFRACTION99.96
3.79-4.340.33921320.27262610X-RAY DIFFRACTION100
4.34-5.470.25621450.23252665X-RAY DIFFRACTION99.93
5.47-73.520.27141240.25922851X-RAY DIFFRACTION99.93

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