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- PDB-6fgp: NMR solution structure of monomeric CCL5 in complex with a doubly... -

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Basic information

Entry
Database: PDB / ID: 6fgp
TitleNMR solution structure of monomeric CCL5 in complex with a doubly-sulfated N-terminal segment of CCR5
Components
  • C-C chemokine receptor type 5
  • C-C motif chemokine 5Chemokine
KeywordsPROTEIN BINDING / chemokine complex NMR
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / chemokine (C-C motif) ligand 5 binding / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / chemokine (C-C motif) ligand 5 binding / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / signaling / positive regulation of activation of Janus kinase activity / chemokine receptor activity / receptor signaling protein tyrosine kinase activator activity / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / CCR chemokine receptor binding / lymphocyte chemotaxis / neutrophil activation / C-C chemokine binding / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / positive regulation of macrophage chemotaxis / negative regulation of viral genome replication / phospholipase activator activity / macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of translational initiation / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of viral genome replication / Binding and entry of HIV virion / cellular response to interleukin-1 / cellular defense response / coreceptor activity / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / cell chemotaxis / neutrophil chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / calcium-mediated signaling / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / intracellular calcium ion homeostasis / response to toxic substance / cellular response to virus / cellular response to type II interferon / : / calcium ion transport / chemotaxis / MAPK cascade / virus receptor activity / cell-cell signaling / cellular response to tumor necrosis factor / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / protein kinase activity / positive regulation of cell migration / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding
Similarity search - Function
CC chemokine receptor 5 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CC chemokine receptor 5 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 5 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsAnglister, J. / Abayev, M.
Funding support Germany, 5items
OrganizationGrant numberCountry
Minerva Foundation Germany
United States - Israel Binational Science Foundation (BSF)
The estate of D. Levinson
Kimmelman Center
National Institutes of HealthGM115749
CitationJournal: FEBS J. / Year: 2018
Title: The solution structure of monomeric CCL5 in complex with a doubly sulfated N-terminal segment of CCR5.
Authors: Abayev, M. / Rodrigues, J.P.G.L.M. / Srivastava, G. / Arshava, B. / Jaremko, L. / Jaremko, M. / Naider, F. / Levitt, M. / Anglister, J.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Sep 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C chemokine receptor type 5
B: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)11,2252
Polymers11,2252
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1070 Å2
ΔGint-1 kcal/mol
Surface area7810 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 106structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide C-C chemokine receptor type 5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 3357.653 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal segment of CCR5, doubly-sulfated at position Y10 and Y14 that were synthesized by solid-phase peptide-synthesis
Source: (synth.) Homo sapiens (human) / References: UniProt: P51681
#2: Protein C-C motif chemokine 5 / Chemokine / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 7866.990 Da / Num. of mol.: 1 / Mutation: i
Source method: isolated from a genetically manipulated source
Details: Chemokine protein (consist P9S and E66S mutations).
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
311isotropic13D HN(CA)CB
321isotropic13D CBCA(CO)NH
331isotropic13D HNCA
341isotropic13D HNCO
251isotropic13D (H)CCH-TOCSY
281isotropic13D CCH-TOCSY
371isotropic13D HCC(CO)NH-TOCSY
161isotropic13D 1H-15N TOCSY
1101isotropic13D 1H-15N NOESY
2141isotropic13D 1H-13C NOESY aliphatic
2151isotropic13D 1H-13C NOESY aromatic
391isotropic12D 1H-1H NOESY (double filter)
3131isotropic12D 1H-1H TOCSY (double filter)
2121isotropic13D 1H-13C NOESY (edited/filtered)

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1120 uM [U-15N] CCL5(P9S)/Nt-CCR5(1-27), 90% H2O/10% D2OCCL5(P9S)/Nt-CCR5(1-27) solutions contained 120 uM CCL5(P9S) with 5-fold molar concentration of Nt-CCR5(1-27) in 130 mM d-acetate buffer, pH 4.8. CCL5(P9S) was either U-15N, U-15N;13C or U-13C labeled. Nt-CCR5(1-27) was unlabeled for all samples.CCL5(P9S)/Nt-CCR5(1-27)90% H2O/10% D2O
solution2120 uM [U-13C] CCL5(P9S)/Nt-CCR5(1-27), 90% H2O/10% D2OCCL5(P9S)/Nt-CCR5(1-27) solutions contained 120 uM CCL5(P9S) with 5-fold molar concentration of Nt-CCR5(1-27) in 130 mM d-acetate buffer, pH 4.8. CCL5(P9S) was either U-15N, U-15N;13C or U-13C labeled. Nt-CCR5(1-27) was unlabeled for all samples.CCL5(P9S)/Nt-CCR5(1-27)90% H2O/10% D2O
solution3120 uM U-15N;13C CCL5(P9S)/Nt-CCR5(1-27), 90% H2O/10% D2OCCL5(P9S)/Nt-CCR5(1-27) solutions contained 120 uM CCL5(P9S) with 5-fold molar concentration of Nt-CCR5(1-27) in 130 mM d-acetate buffer, pH 4.8. CCL5(P9S) was either U-15N, U-15N;13C or U-13C labeled. Nt-CCR5(1-27) was unlabeled for all samples.CCL5(P9S)/Nt-CCR5(1-27)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
120 uMCCL5(P9S)/Nt-CCR5(1-27)[U-15N]1
120 uMCCL5(P9S)/Nt-CCR5(1-27)[U-13C]2
120 uMCCL5(P9S)/Nt-CCR5(1-27)U-15N;13C3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1130 mMU-15N4.8 1 atm310 K
2130 mMU-13C4.8 1 atm310 K
3130 mMU-15N;13C4.8 1 atm310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
HADDOCKBonvinrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 106 / Conformers submitted total number: 10

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