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- PDB-2kol: Solution structure of human SDF1-alpha H25R -

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Basic information

Entry
Database: PDB / ID: 2kol
TitleSolution structure of human SDF1-alpha H25R
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE / chemokine / SDF1-alpha / Chemotaxis / Growth factor
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / telencephalon cell migration / chemokine receptor binding / response to ultrasound / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / telencephalon cell migration / chemokine receptor binding / response to ultrasound / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / chemokine-mediated signaling pathway / cellular response to chemokine / positive regulation of monocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / blood circulation / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / animal organ regeneration / positive regulation of T cell migration / detection of mechanical stimulus involved in sensory perception of pain / Nuclear signaling by ERBB4 / positive regulation of endothelial cell proliferation / positive regulation of cell adhesion / positive regulation of neuron differentiation / axon guidance / adult locomotory behavior / cell chemotaxis / growth factor activity / defense response / response to virus / response to peptide hormone / intracellular calcium ion homeostasis / neuron migration / chemotaxis / integrin binding / : / G alpha (i) signalling events / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
CXC Chemokine domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model 1
AuthorsVolkman, B.F. / Ziarek, J.J. / Peterson, F.C. / Veldkamp, C.T.
CitationJournal: To be Published
Title: Solution structure of human SDF1-alpha H25R
Authors: Ziarek, J.J. / Veldkamp, C.T. / Peterson, F.C. / Volkman, B.F.
History
DepositionSep 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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)7,9981
Polymers7,9981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Stromal cell-derived factor 1 / SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Pre-B cell growth-stimulating factor / PBSF / hIRH / ...SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Pre-B cell growth-stimulating factor / PBSF / hIRH / SDF-1-beta(3-72) / SDF-1-alpha(3-67)


Mass: 7997.507 Da / Num. of mol.: 1 / Fragment: SDF-1-alpha, residues 22-89 / Mutation: H25R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: P48061
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 3.3 mM [U-100% 13C; U-100% 15N] SDF1a H25R, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.3 mMSDF1a H25R-1[U-100% 13C; U-100% 15N]1
25 mMMES-2[U-99% 2H]1
0.02 %sodium azide-31
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1430 NOE CONSTRAINTS (339 INTRA, 388 SEQUENTIAL, 263 MEDIUM, AND 440 LONG RANGE) AND 65 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1430 / NOE intraresidue total count: 339 / NOE long range total count: 440 / NOE medium range total count: 263 / NOE sequential total count: 388
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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