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- PDB-5t1a: Structure of CC Chemokine Receptor 2 with Orthosteric and Alloste... -

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Basic information

Entry
Database: PDB / ID: 5t1a
TitleStructure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists
ComponentsChimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme
KeywordsSIGNALING PROTEIN / C-C Chemokine Receptor type 2 / dual antagonist / intracellular allosteric antagonist / cooperative binding / lipidic cubic phase / membrane protein / GPCR / Structural Genomics / PSI-2 / Protein Structure Initiative / GPCR Network
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 / viral release from host cell by cytolysis / positive regulation of interleukin-2 production / cell chemotaxis / positive regulation of synaptic transmission, glutamatergic / negative regulation of angiogenesis / peptidoglycan catabolic process / 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 / cell wall macromolecule catabolic process / positive regulation of tumor necrosis factor production / lysozyme / lysozyme activity / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / regulation of inflammatory response / perikaryon / host cell cytoplasm / defense response to bacterium / immune response / inflammatory response / 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 / Chemokine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...CC chemokine receptor 2 / Chemokine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-73R / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-VT5 / Endolysin / C-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å
AuthorsZheng, Y. / Qin, L. / Ortiz Zacarias, N.V. / de Vries, H. / Han, G.W. / Gustavsson, M. / Dabros, M. / Zhao, C. / Cherney, R.J. / Carter, P. ...Zheng, Y. / Qin, L. / Ortiz Zacarias, N.V. / de Vries, H. / Han, G.W. / Gustavsson, M. / Dabros, M. / Zhao, C. / Cherney, R.J. / Carter, P. / Stamos, D. / Abagyan, R. / Cherezov, V. / Stevens, R.C. / IJzerman, A.P. / Heitman, L.H. / Tebben, A. / Kufareva, I. / Handel, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI122211 United States
CitationJournal: Nature / Year: 2016
Title: Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists.
Authors: Zheng, Y. / Qin, L. / Zacarias, N.V. / de Vries, H. / Han, G.W. / Gustavsson, M. / Dabros, M. / Zhao, C. / Cherney, R.J. / Carter, P. / Stamos, D. / Abagyan, R. / Cherezov, V. / Stevens, R.C. ...Authors: Zheng, Y. / Qin, L. / Zacarias, N.V. / de Vries, H. / Han, G.W. / Gustavsson, M. / Dabros, M. / Zhao, C. / Cherney, R.J. / Carter, P. / Stamos, D. / Abagyan, R. / Cherezov, V. / Stevens, R.C. / IJzerman, A.P. / Heitman, L.H. / Tebben, A. / Kufareva, I. / Handel, T.M.
History
DepositionAug 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Jan 4, 2017Group: Database references
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5789
Polymers57,9281
Non-polymers1,6508
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-93 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.230, 64.690, 169.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme / / CCR2 / Monocyte chemoattractant protein 1 receptor / MCP-1-R


Mass: 57928.355 Da / Num. of mol.: 1
Fragment: UNP P41597-2 residues 2-328 with UNP P00720 residues 2-161 inserted after residues 233
Mutation: L226S, K227R, T228A, L229S, L230K, R231S, C232R, R233I, N234P, E235P, K236S, K237R, R238E, H238K, R239K, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CCR2, CMKBR2, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41597, UniProt: D9IEF7, lysozyme

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Non-polymers , 6 types, 25 molecules

#2: Chemical ChemComp-73R / (3S)-1-{(1S,2R,4R)-4-[methyl(propan-2-yl)amino]-2-propylcyclohexyl}-3-{[6-(trifluoromethyl)quinazolin-4-yl]amino}pyrrolidin-2-one


Mass: 491.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36F3N5O
#3: Chemical ChemComp-VT5 / (2~{R})-1-(4-chloranyl-2-fluoranyl-phenyl)-2-cyclohexyl-3-ethanoyl-4-oxidanyl-2~{H}-pyrrol-5-one


Mass: 351.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19ClFNO3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.81 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.1
Details: Lipidic cubic phase made of monoolein and cholesterol, 100 mM 2-(N-morpholino)ethanesulfonic acid, pH 6.5, 30-32% (v/v) PEG 400, 75-85 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 16, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.8→23.321 Å / Num. obs: 15550 / % possible obs: 93.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.35 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.103 / Rrim(I) all: 0.264 / Net I/σ(I): 6.9 / Num. measured all: 82110 / Scaling rejects: 501
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.951.81.132292215830.3460.8611.4320.866.6
8.85-48.65.40.08131275790.9950.0380.092695.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.806→24.321 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 742 5.12 %Random selection
Rwork0.2335 13745 --
obs0.2355 14487 87.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.63 Å2 / Biso mean: 41.2114 Å2 / Biso min: 3.08 Å2
Refinement stepCycle: final / Resolution: 2.806→24.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 105 17 3580
Biso mean--40.64 22.14 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033643
X-RAY DIFFRACTIONf_angle_d0.8454961
X-RAY DIFFRACTIONf_chiral_restr0.032577
X-RAY DIFFRACTIONf_plane_restr0.003603
X-RAY DIFFRACTIONf_dihedral_angle_d12.8511267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8057-3.0220.3926870.32351157124438
3.022-3.32540.33431550.30363062321799
3.3254-3.8050.30321690.243531263295100
3.805-4.78790.25811530.2033140329399
4.7879-24.32150.21411780.20553260343899
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)
11.13360.1155-0.38611.1581-0.36471.92870.03430.14410.126-0.13010.0035-0.0079-0.1247-0.0548-0.07120.36760.00070.02080.31140.02160.092312.672423.8183170.4808
20.6985-0.4384-0.70291.2603-0.14691.5096-0.0174-0.31790.18160.33630.1725-0.47020.01380.34010.150.49790.0472-0.09430.4515-0.0229-0.00088.981112.4267214.5599
31.52160.02710.05711.3690.10163.2509-0.130.3555-0.1375-0.00370.0876-0.0406-0.1402-0.1438-0.13840.3414-0.00210.02220.4002-0.0679-0.05322.346520.7634171.3347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 233 )A37 - 233
2X-RAY DIFFRACTION2chain 'A' and (resid 1002 through 1162 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 320 )A234 - 320

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