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

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Basic information

Entry
Database: PDB / ID: 6gps
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 / positive regulation of NMDA glutamate receptor activity / monocyte extravasation / CCR2 chemokine receptor binding / regulation of vascular endothelial growth factor production / negative regulation of type 2 immune response / Beta defensins / positive regulation of monocyte extravasation / regulation of macrophage migration / macrophage migration / neutrophil clearance / regulation of T cell cytokine production / alkane catabolic process / positive regulation of leukocyte tethering or rolling / chemokine receptor activity / positive regulation of T-helper 1 type immune response / positive regulation of T cell chemotaxis / inflammatory response to wounding / positive regulation of alpha-beta T cell proliferation / C-C chemokine receptor activity / negative regulation of adenylate cyclase activity / chemokine-mediated signaling pathway / C-C chemokine binding / cellular homeostasis / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / dendritic cell chemotaxis / regulation of T cell differentiation / Interleukin-10 signaling / monocyte chemotaxis / hemopoiesis / humoral immune response / blood vessel remodeling / cell surface receptor signaling pathway via JAK-STAT / cellular defense response / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of interleukin-2 production / positive regulation of synaptic transmission, glutamatergic / negative regulation of angiogenesis / cell chemotaxis / calcium-mediated signaling / cytokine-mediated signaling pathway / response to wounding / positive regulation of T cell activation / positive regulation of type II interferon production / fibrillar center / intracellular calcium ion homeostasis / positive regulation of inflammatory response / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / G alpha (i) signalling events / perikaryon / electron transfer activity / immune response / inflammatory response / iron ion binding / external side of plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 2 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Chemokine receptor family / Rubredoxin-like domain / Rubredoxin-like domain profile. ...CC chemokine receptor 2 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Chemokine receptor family / Rubredoxin-like domain / Rubredoxin-like domain profile. / : / 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)
Similarity search - Domain/homology
Chem-F7N / Rubredoxin / C-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsPautsch, A. / Schnapp, G.
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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,8143
Polymers48,2781
Non-polymers5362
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.500, 61.200, 123.570
Angle α, β, γ (deg.)90.00, 97.66, 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: 48278.184 Da / Num. of mol.: 1
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,RUBREDOXIN ...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,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,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
Mutation: N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, ...Mutation: N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E
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-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.: 1 / Source method: obtained synthetically / Formula: C24H35F3N3O3
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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: reconstituted into lipidic cubic phase (LCP) by mixing with 9.9 MAG (Monoolein, Sigma) using a syringe mixer as described previously (Caffrey and Cherezov, 2009). 35 % (w/w) of the receptor ...Details: reconstituted into lipidic cubic phase (LCP) by mixing with 9.9 MAG (Monoolein, Sigma) using a syringe mixer as described previously (Caffrey and Cherezov, 2009). 35 % (w/w) of the receptor solution was mixed with 61.5 % monoolein (w/w), additionally supplemented with 3.5 % cholesterol (w/w). Crystallization trials were performed in 96-well glass sandwich plates (Molecular Dimensions). The LCP drops were pipetted in a bolus volume of 50 nl using a gryphon robot and overlaid with 800 nl of precipitant solution per well. Diffracting quality crystals were obtained with 0.1 M MES pH 6.0, 0.2 M ammonium acetate and 40 % PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→43.29 Å / Num. obs: 8271 / % possible obs: 95 % / Redundancy: 3.1 % / Biso Wilson estimate: 99.49 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.087 / Net I/σ(I): 5.7
Reflection shellResolution: 3.3→3.57 Å / Mean I/σ(I) obs: 3 / CC1/2: 0.479

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementResolution: 3.3→37.89 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.783 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.545
RfactorNum. reflection% reflectionSelection details
Rfree0.296 372 4.5 %RANDOM
Rwork0.243 ---
obs0.245 8261 94.6 %-
Displacement parametersBiso mean: 111.76 Å2
Baniso -1Baniso -2Baniso -3
1-24.1642 Å20 Å27.6771 Å2
2---34.1146 Å20 Å2
3---9.9504 Å2
Refine analyzeLuzzati coordinate error obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 3.3→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 34 0 2683
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.779941HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1194SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes810HARMONIC5
X-RAY DIFFRACTIONt_it5481HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion16.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
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_contact5440SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.37 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2583 -4.36 %
Rwork0.2355 439 -
all0.2365 459 -
obs--93.09 %
Refinement TLS params.Method: refined / Origin x: 11.029 Å / Origin y: -6.9402 Å / Origin z: -32.6241 Å
111213212223313233
T-0.0155 Å2-0.0086 Å2-0.0828 Å2-0.0599 Å2-0.0517 Å2---0.1055 Å2
L1.1124 °2-0.2819 °20.3518 °2-0 °2-0.7546 °2--0.5932 °2
S0.0108 Å °-0.0257 Å °-0.0057 Å °-0.0182 Å °-0.0316 Å °-0.0184 Å °0.0245 Å °-0.0244 Å °0.0207 Å °
Refinement TLS groupSelection details: { A|* }

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