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- PDB-6qzh: Structure of the human CC Chemokine Receptor 7 in complex with th... -

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Basic information

Entry
Database: PDB / ID: 6qzh
TitleStructure of the human CC Chemokine Receptor 7 in complex with the intracellular allosteric antagonist Cmp2105 and the insertion protein Sialidase NanA
ComponentsC-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7
KeywordsSIGNALING PROTEIN / GPCR / Chemokine Receptor / Small molecule / Allosteric modulator / Insertion protein
Function / homology
Function and homology information


positive regulation of hypersensitivity / chemokine (C-C motif) ligand 19 binding / chemokine (C-C motif) ligand 21 binding / C-C motif chemokine 19 receptor activity / C-C motif chemokine 21 receptor activity / positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation / regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / positive regulation of immunological synapse formation / positive regulation of T cell costimulation ...positive regulation of hypersensitivity / chemokine (C-C motif) ligand 19 binding / chemokine (C-C motif) ligand 21 binding / C-C motif chemokine 19 receptor activity / C-C motif chemokine 21 receptor activity / positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation / regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / positive regulation of immunological synapse formation / positive regulation of T cell costimulation / mature conventional dendritic cell differentiation / positive regulation of humoral immune response / : / lymphocyte migration into lymph node / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / positive regulation of dendritic cell chemotaxis / establishment of T cell polarity / regulation of interleukin-1 beta production / chemokine binding / regulation of type II interferon production / positive regulation of pseudopodium assembly / negative thymic T cell selection / C-C chemokine receptor activity / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / C-C chemokine binding / ruffle organization / ganglioside catabolic process / oligosaccharide catabolic process / activation of GTPase activity / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / positive regulation of cell motility / dendritic cell chemotaxis / positive regulation of filopodium assembly / positive regulation of cell-matrix adhesion / response to nitric oxide / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / positive regulation of actin filament polymerization / exo-alpha-sialidase / positive regulation of T cell receptor signaling pathway / cellular response to cytokine stimulus / positive regulation of cell adhesion / homeostasis of number of cells / positive regulation of protein kinase activity / release of sequestered calcium ion into cytosol / positive regulation of interleukin-12 production / cell chemotaxis / G protein-coupled receptor activity / calcium-mediated signaling / positive regulation of JNK cascade / chemotaxis / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / intracellular membrane-bounded organelle / cell surface / mitochondrion / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 7 / BNR/Asp-box repeat / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / Chemokine receptor family / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family ...CC chemokine receptor 7 / BNR/Asp-box repeat / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / Chemokine receptor family / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Sialidase superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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) / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-JLW / TRIETHYLENE GLYCOL / D(-)-TARTARIC ACID / C-C chemokine receptor type 7 / Sialidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJaeger, K. / Bruenle, S. / Weinert, T. / Guba, W. / Muehle, J. / Miyazaki, T. / Weber, M. / Furrer, A. / Haenggi, N. / Tetaz, T. ...Jaeger, K. / Bruenle, S. / Weinert, T. / Guba, W. / Muehle, J. / Miyazaki, T. / Weber, M. / Furrer, A. / Haenggi, N. / Tetaz, T. / Huang, C.Y. / Mattle, D. / Vonach, J.M. / Gast, A. / Kuglstatter, A. / Rudolph, M.G. / Nogly, P. / Benz, J. / Dawson, R.J.P. / Standfuss, J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Commission701647
Swiss National Science Foundation31003A_159558 Switzerland
CitationJournal: Cell / Year: 2019
Title: Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7.
Authors: Jaeger, K. / Bruenle, S. / Weinert, T. / Guba, W. / Muehle, J. / Miyazaki, T. / Weber, M. / Furrer, A. / Haenggi, N. / Tetaz, T. / Huang, C.Y. / Mattle, D. / Vonach, J.M. / Gast, A. / ...Authors: Jaeger, K. / Bruenle, S. / Weinert, T. / Guba, W. / Muehle, J. / Miyazaki, T. / Weber, M. / Furrer, A. / Haenggi, N. / Tetaz, T. / Huang, C.Y. / Mattle, D. / Vonach, J.M. / Gast, A. / Kuglstatter, A. / Rudolph, M.G. / Nogly, P. / Benz, J. / Dawson, R.J.P. / Standfuss, J.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec
Revision 1.2Jan 24, 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
A: C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2896
Polymers88,3411
Non-polymers9495
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-7 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.124, 128.809, 100.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7 / CCR-7 / BLR2 / CDw197 / Epstein-Barr virus-induced G-protein coupled receptor 1 / EBV-induced G- ...CCR-7 / BLR2 / CDw197 / Epstein-Barr virus-induced G-protein coupled receptor 1 / EBV-induced G-protein coupled receptor 1 / MIP-3 beta receptor / Neuraminidase A / CCR-7 / BLR2 / CDw197 / Epstein-Barr virus-induced G-protein coupled receptor 1 / EBV-induced G-protein coupled receptor 1 / MIP-3 beta receptor


Mass: 88340.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: CCR7, CMKBR7, EBI1, EVI1, nanA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P32248, UniProt: P62575, exo-alpha-sialidase

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-JLW / 3-[[4-[[(1~{R})-2,2-dimethyl-1-(5-methylfuran-2-yl)propyl]amino]-1,1-bis(oxidanylidene)-1,2,5-thiadiazol-3-yl]amino]-~{N},~{N},6-trimethyl-2-oxidanyl-benzamide


Mass: 475.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N5O5S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 200 mM MES pH 6.0, 100 mM ammonium tartrate dibasic, 23-27 % (v/v) PEG 500 MME, 1 mM - 5 mM GSH/GSSG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0, 2.066
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.0661
ReflectionResolution: 2.1→79.3 Å / Num. obs: 31344 / % possible obs: 53.3 % / Redundancy: 27.4 % / CC1/2: 0.97 / Rpim(I) all: 0.1 / Net I/av σ(I): 8.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.4 Å / Redundancy: 33.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1568 / CC1/2: 0.64 / Rpim(I) all: 0.92 / % possible all: 8.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RWS

4rws


Resolution: 2.1→54.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2416 --
Rwork0.1877 --
obs-31344 52.76 %
Refinement stepCycle: LAST / Resolution: 2.1→54.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 60 149 6080

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