[English] 日本語
Yorodumi
- PDB-6qzh: Structure of the human CC Chemokine Receptor 7 in complex with th... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of humoral immune response / lymphocyte migration into lymph node / mature conventional dendritic cell differentiation / positive regulation of dendritic cell antigen processing and presentation / establishment of T cell polarity / positive regulation of dendritic cell chemotaxis / regulation of interleukin-1 beta production / regulation of type II interferon production / positive regulation of pseudopodium assembly / negative thymic T cell selection / negative regulation of interleukin-12 production / C-C chemokine receptor activity / negative regulation of dendritic cell apoptotic process / ruffle organization / ganglioside catabolic process / positive regulation of neutrophil chemotaxis / oligosaccharide catabolic process / Chemokine receptors bind chemokines / positive regulation of filopodium assembly / dendritic cell chemotaxis / positive regulation of cell-matrix adhesion / response to nitric oxide / positive regulation of cell motility / positive regulation of actin filament polymerization / exo-alpha-sialidase / cellular response to cytokine stimulus / positive regulation of T cell receptor signaling pathway / exo-alpha-sialidase activity / homeostasis of number of cells / positive regulation of protein kinase activity / response to prostaglandin E / release of sequestered calcium ion into cytosol / positive regulation of interleukin-12 production / positive regulation of cell adhesion / cell chemotaxis / positive regulation of JNK cascade / calcium-mediated signaling / G protein-coupled receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / immune response / G protein-coupled receptor signaling pathway / inflammatory response / 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 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / Chemokine receptor family / BNR repeat-like domain / Laminin G domain / Laminin G domain ...CC chemokine receptor 7 / : / BNR/Asp-box repeat / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / 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 / Gram-positive cocci surface proteins LPxTG motif profile. / Sialidase superfamily / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more