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- PDB-5l7m: Murin CXCL13 solution structure -

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Basic information

Entry
Database: PDB / ID: 5l7m
TitleMurin CXCL13 solution structure
ComponentsC-X-C motif chemokine 13
KeywordsSIGNALING PROTEIN / Chemokine structure / N-terminal domain / GAG binding
Function / homology
Function and homology information


B cell chemotaxis across high endothelial venule / lymphocyte chemotaxis across high endothelial venule / CXCR5 chemokine receptor binding / endothelial cell chemotaxis to fibroblast growth factor / negative regulation of endothelial cell chemotaxis to fibroblast growth factor / CCR10 chemokine receptor binding / Chemokine receptors bind chemokines / B cell chemotaxis / CXCR3 chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin ...B cell chemotaxis across high endothelial venule / lymphocyte chemotaxis across high endothelial venule / CXCR5 chemokine receptor binding / endothelial cell chemotaxis to fibroblast growth factor / negative regulation of endothelial cell chemotaxis to fibroblast growth factor / CCR10 chemokine receptor binding / Chemokine receptors bind chemokines / B cell chemotaxis / CXCR3 chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / G alpha (i) signalling events / positive regulation of T cell chemotaxis / CXCR chemokine receptor binding / positive regulation of integrin activation / chemokine-mediated signaling pathway / activation of GTPase activity / chemokine activity / fibroblast growth factor binding / lymph node development / neutrophil chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / heparin binding / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / killing of cells of another organism / receptor ligand activity / cell surface receptor signaling pathway / defense response to bacterium / inflammatory response / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
Similarity search - Domain/homology
C-X-C motif chemokine 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMonneau, Y.R. / Lortat-Jacob, H.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Open Biol / Year: 2017
Title: Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains.
Authors: Monneau, Y.R. / Luo, L. / Sankaranarayanan, N.V. / Nagarajan, B. / Vives, R.R. / Baleux, F. / Desai, U.R. / Arenzana-Seidedos, F. / Lortat-Jacob, H.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-X-C motif chemokine 13


Theoretical massNumber of molelcules
Total (without water)9,8081
Polymers9,8081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8230 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein C-X-C motif chemokine 13 / B lymphocyte chemoattractant / CXC chemokine BLC / Small-inducible cytokine B13


Mass: 9807.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cxcl13, Blc, Scyb13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: O55038

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1141isotropic12D 1H-15N HSQC
122isotropic13D HNCA
1132isotropic13D HN(CA)CB
142isotropic12D 1H-13C HSQC aliphatic
152isotropic12D 1H-13C HSQC aromatic
162isotropic13D (H)CCH-TOCSY
172isotropic13D (H)CCH-TOCSY
181isotropic23D 1H-15N TOCSY-HSQC
191isotropic23D 1H-15N NOESY-HSQC
1102isotropic12D (HB)CB(CG)(CD)HD
1112isotropic13D 1H-13C NOESY-HMQC
1123isotropic33D 1H-15N NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1850 uM [U-15N] CXCL13, 90% H2O/10% D2OdN-CXCL13-N90% H2O/10% D2O
solution2560 uM U-[15N,13C] CXCL13, 90% H2O/10% D2OdN-CXCL13-CN90% H2O/10% D2O
solution3250 uM [U-15N] CXCL13, 90% H2O/10% D2OCXC13-N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
850 uMCXCL13[U-15N]1
560 uMCXCL13U-[15N,13C]2
250 uMCXCL13[U-15N]3
Sample conditionsDetails: 20 mM KP 100 mM NaCl / Ionic strength: 120 mM / Label: all / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III8503

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: in presence of water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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