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- PDB-2k01: Structure of a locked SDF1 dimer -

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Basic information

Entry
Database: PDB / ID: 2k01
TitleStructure of a locked SDF1 dimer
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / chemokine / sulfotyrosine / locked dimer / Alternative splicing / Chemotaxis / Growth factor / Secreted
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, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Veldkamp, C.T. / Peterson, F.C.
CitationJournal: Sci.Signal. / Year: 2008
Title: Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12
Authors: Veldkamp, C.T. / Seibert, C. / Peterson, F.C. / De la Cruz, N.B. / Haugner, J.C. / Basnet, H. / Sakmar, T.P. / Volkman, B.F.
History
DepositionJan 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 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
C: Stromal cell-derived factor 1


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,3782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 / C-X-C motif chemokine 12 / Pre-B cell growth-stimulating factor / PBSF / hIRH


Mass: 8188.760 Da / Num. of mol.: 2 / Fragment: SDF-1-alpha(3-67) domain / Mutation: L36C,A65C
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: 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.620 mM / Component: CXCL12/SDF1-alpha / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,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
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, 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: CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND ...Details: CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS., CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS.
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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