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- PDB-6ehz: NMR solution structure of murine CXCL12 gamma isoform -

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Basic information

Entry
Database: PDB / ID: 6ehz
TitleNMR solution structure of murine CXCL12 gamma isoform
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE / Stromall cell derived factor 1 gamma isoform Chemokine
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / positive regulation of monocyte chemotaxis / chemokine activity / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / adult locomotory behavior / neuron migration / growth factor activity / response to radiation / defense response / response to peptide hormone / integrin binding / response to heat / response to hypoxia / immune response / extracellular space / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Stromal cell-derived factor 1 / 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 12
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsLaguri, C. / Lortat-Jacob, H. / SImorre, J.P.
CitationJournal: Glycobiology / Year: 2021
Title: Deciphering the structural attributes of protein-heparan sulfate interactions using chemo-enzymatic approaches and NMR spectroscopy
Authors: Prechoux, A. / Simorre, J.P. / Lortat-Jacob, H. / Laguri, C.
History
DepositionSep 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Structure summary / Category: entity / pdbx_nmr_software / Item: _entity.formula_weight / _pdbx_nmr_software.name
Revision 1.2Mar 17, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stromal cell-derived factor 1


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9000 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Stromal cell-derived factor 1 /


Mass: 11611.919 Da / Num. of mol.: 1 / Fragment: UNP residues 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cxcl12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7BX38

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY
132isotropic13D (H)CCH-TOCSY
142isotropic13D H(CCO)NH
152isotropic13D 1H-13C NOESY aromatic
162isotropic13D 1H-13C NOESY methyls

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] CXCL12 gamma isoform, 90% H2O/10% D2O
Label: standard 13C15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: CXCL12 gamma isoform / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 20 mM NaH2PO4 pH 5.7, 10% D2O, 0.01% NaN3 / Ionic strength: 20 mM / Ionic strength err: 3 / Label: standard / pH: 5.7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 303 K / Temperature err: 2

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NMR measurement

NMR spectrometerType: Varian 600 Direct Drive / Manufacturer: Varian / Model: 600 Direct Drive / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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