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- PDB-5izb: Murin CXCL13 solution structure featuring a folded N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5izb
TitleMurin CXCL13 solution structure featuring a folded N-terminal domain
ComponentsC-X-C motif chemokine 13
KeywordsSIGNALING PROTEIN / Chemokine structure N-terminal domain conformational exchange
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 / activation of GTPase activity / chemokine-mediated signaling pathway / 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 / killing of cells of another organism / cellular response to lipopolysaccharide / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
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: To be published
Title: Murin CXCL13 solution structure featuring a folded N-terminal domain
Authors: Monneau, Y.R. / Luo, L. / Vives, R. / Arenzana-Seidedos, F. / Lortat-Jacob, H.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_sheet_hbond.range_2_auth_comp_id ..._pdbx_audit_support.funding_organization / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conn.pdbx_dist_value
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_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)9,9391
Polymers9,9391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures 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: 9938.868 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
111isotropic13D 15N-edited NOESY
122isotropic33D 13C-edited NOESY
132isotropic33D 13C-HMQC-NOESY-13C,1H-HMQC
143isotropic43D HN(CA)CB
153isotropic43D HNCA
163isotropic43D CBCA(CO)NH
1183isotropic43D HN(CO)CA
173isotropic43D HNCO
183isotropic43D HACACO
193isotropic43D (H)CCH-TOCSY
1103isotropic43D (H)CCH-TOCSY
1112isotropic22D 1H-13C HSQC aliphatic
1122isotropic22D 1H-13C HSQC aromatic
1133isotropic42D 1H-15N HSQC
1144isotropic12D 1H-13C CT-HSQC aliphatic
1154isotropic22D COSYdqf
1164isotropic22D TOCSY
1172isotropic42D CBCGCDHD

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1850 uM U-[15N] CXCL13, 95% H2O/5% D2O15Nnoesy95% H2O/5% D2O
solution2280 uM U-[13C,15N] CXCL13, 100% D2O13Cnoesy100% D2O
solution3280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2Oassignment95% H2O/5% D2O
solution4280 uM [U-10% 13C; U-100% 15N] CXCL13, 100% D2Oaro+met100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
850 uMCXCL13[U-15N]1
280 uMCXCL13U-[13C,15N]2
280 uMCXCL13U-[13C,15N]3
280 uMCXCL13[U-10% 13C; U-100% 15N]4
Sample conditionsDetails: 20 mM Phosphate buffer 100 mM NaCl / Ionic strength: 120 mM / Label: 1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001cryoprobe
Bruker AVANCE IIIBrukerAVANCE III7002cryoprobe
Bruker AVANCE IIIBrukerAVANCE III9503cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8504cryoprobe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, P., Mumenthaler, C., & Wuthrich, K., Herrmann, T.,structure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRFAM-SPARKYLee et al. Bioinformatics 2015 Apr 15; 31(8):1325-7chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: in presence of water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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