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- PDB-6gpx: CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 -

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Basic information

Entry
Database: PDB / ID: 6gpx
TitleCRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812
ComponentsC-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
KeywordsSIGNALING PROTEIN / GPCR / Signalling / Drug-design
Function / homology
Function and homology information


T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration ...T-helper 17 cell chemotaxis / chemokine (C-C motif) ligand 2 binding / chemokine (C-C motif) ligand 12 binding / negative regulation of eosinophil degranulation / positive regulation of immune complex clearance by monocytes and macrophages / positive regulation of CD8-positive, alpha-beta T cell extravasation / positive regulation of astrocyte chemotaxis / leukocyte adhesion to vascular endothelial cell / chemokine (C-C motif) ligand 7 binding / positive regulation of thymocyte migration / positive regulation of hematopoietic stem cell migration / monocyte extravasation / CCR2 chemokine receptor binding / negative regulation of type 2 immune response / regulation of vascular endothelial growth factor production / positive regulation of NMDA glutamate receptor activity / Beta defensins / positive regulation of monocyte extravasation / macrophage migration / regulation of T cell cytokine production / regulation of macrophage migration / neutrophil clearance / positive regulation of leukocyte tethering or rolling / chemokine receptor activity / positive regulation of T-helper 1 type immune response / inflammatory response to wounding / positive regulation of T cell chemotaxis / positive regulation of alpha-beta T cell proliferation / C-C chemokine receptor activity / C-C chemokine binding / negative regulation of adenylate cyclase activity / cellular homeostasis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / dendritic cell chemotaxis / regulation of T cell differentiation / Interleukin-10 signaling / monocyte chemotaxis / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / hemopoiesis / blood vessel remodeling / cellular defense response / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of interleukin-2 production / cell chemotaxis / positive regulation of synaptic transmission, glutamatergic / negative regulation of angiogenesis / calcium-mediated signaling / intracellular calcium ion homeostasis / fibrillar center / positive regulation of inflammatory response / response to wounding / cytokine-mediated signaling pathway / chemotaxis / positive regulation of T cell activation / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / regulation of inflammatory response / perikaryon / electron transfer activity / immune response / inflammatory response / iron ion binding / external side of plasma membrane / dendrite / neuronal cell body / perinuclear region of cytoplasm / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CC chemokine receptor 2 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rhopdopsin 7-helix transmembrane proteins ...CC chemokine receptor 2 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-F7N / OLEIC ACID / Rubredoxin / C-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsPautsch, A. / Schnapp, G. / Cheng, R. / Apel, A.
CitationJournal: Structure / Year: 2019
Title: Crystal Structure of CC Chemokine Receptor 2A in Complex with an Orthosteric Antagonist Provides Insights for the Design of Selective Antagonists.
Authors: Apel, A.K. / Cheng, R.K.Y. / Tautermann, C.S. / Brauchle, M. / Huang, C.Y. / Pautsch, A. / Hennig, M. / Nar, H. / Schnapp, G.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
B: C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,27019
Polymers79,3092
Non-polymers4,96117
Water1,15364
1
A: C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,29814
Polymers39,6551
Non-polymers3,64313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9735
Polymers39,6551
Non-polymers1,3184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.570, 64.550, 131.200
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2 / CCR2 / Monocyte chemoattractant protein 1 receptor / MCP-1-R / Rd / CCR2 / Monocyte chemoattractant ...CCR2 / Monocyte chemoattractant protein 1 receptor / MCP-1-R / Rd / CCR2 / Monocyte chemoattractant protein 1 receptor / MCP-1-R


Mass: 39654.602 Da / Num. of mol.: 2
Fragment: RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR2, CMKBR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41597, UniProt: P00268
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-F7N / [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium


Mass: 470.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H35F3N3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using ...Details: protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 25298 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 57.64 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.55 / Net I/σ(I): 6.93
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 1.17 / CC1/2: 0.656 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing
RefinementResolution: 2.7→39.9 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.555 / SU Rfree Blow DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1266 5 %RANDOM
Rwork0.23 ---
obs0.231 25329 100 %-
Displacement parametersBiso mean: 64.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.9364 Å20 Å2-3.4602 Å2
2---14.9287 Å20 Å2
3---15.865 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 276 64 5035
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8518636HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2294SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1484HARMONIC5
X-RAY DIFFRACTIONt_it10264HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion16.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion659SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10589SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.72 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2793 -4.93 %
Rwork0.2263 482 -
all0.2289 507 -
obs--99.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2256-0.22470.22560.4235-0.31732.1827-0.02020.0775-0.041-0.00980.0917-0.09220.09770.0158-0.0715-0.0612-0.05880.03150.03960.0023-0.197859.73296.701433.1882
20.55690.3767-0.1920.65280.20322.71090.01680.02620.0044-0.0307-0.0219-0.0174-0.2417-0.22280.0051-0.0650.02130.00810.03480.0367-0.196236.292924.221339.1113
30.7688-0.1621-0.5130.8585-0.5727-0.02160.00460.00450.00210.0060.00340.0033-0.02210.0383-0.0081-0.05970.0217-0.0112-0.0248-0.0010.020153.905510.97247.7594
40-0.8785-0.00940-0.21990.89450.0004-0.0081-0.00610.0024-0.0111-0.0058-0.0079-0.02620.0107-0.00250.0045-0.0080.00110.0073-0.01345.097610.358752.6619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ X|* }

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