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- PDB-2k04: Structure of SDF1 in complex with the CXCR4 N-terminus containing... -

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Basic information

Entry
Database: PDB / ID: 2k04
TitleStructure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
Components
  • C-X-C chemokine receptor type 4
  • Stromal cell-derived factor 1
KeywordsCYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / CXCR4 / chemokine / locked dimer / Alternative splicing / Chemotaxis / Growth factor / Secreted / G-protein coupled receptor / Glycoprotein / Host-virus interaction / Membrane / Receptor / Sulfation / Transducer / Transmembrane
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / regulation of actin polymerization or depolymerization / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / C-C chemokine receptor activity / endothelial tube morphogenesis / positive regulation of dopamine secretion / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / positive regulation of chemotaxis / regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / induction of positive chemotaxis / integrin activation / positive regulation of dendrite extension / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / anchoring junction / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / positive regulation of calcium ion import / epithelial cell development / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / regulation of calcium ion transport / positive regulation of cell adhesion / positive regulation of T cell migration / Binding and entry of HIV virion / animal organ regeneration / Nuclear signaling by ERBB4 / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / neurogenesis / cell chemotaxis / adult locomotory behavior / response to activity / ubiquitin binding / G protein-coupled receptor activity / axon guidance / calcium-mediated signaling / brain development / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / cellular response to xenobiotic stimulus / late endosome / integrin binding / virus receptor activity / actin binding / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / collagen-containing extracellular matrix / Estrogen-dependent gene expression / lysosome / response to hypoxia / early endosome / cell adhesion / positive regulation of cell migration / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Stromal cell-derived factor 1 / CXC Chemokine domain / Chemokine receptor family / 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 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Stromal cell-derived factor 1 / CXC Chemokine domain / Chemokine receptor family / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Stromal cell-derived factor 1 / C-X-C chemokine receptor type 4
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.
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 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly ...pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_related.db_name
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 1.4Oct 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 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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
B: C-X-C chemokine receptor type 4
C: Stromal cell-derived factor 1
D: C-X-C chemokine receptor type 4


Theoretical massNumber of molelcules
Total (without water)25,4154
Polymers25,4154
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8690 Å2
ΔGint-43 kcal/mol
Surface area12430 Å2
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): SD13009[pREP4] / References: UniProt: P48061
#2: Protein/peptide C-X-C chemokine receptor type 4 / CXC-R4 / CXCR-4 / Stromal cell- derived factor 1 receptor / SDF-1 receptor / Fusin / Leukocyte- ...CXC-R4 / CXCR-4 / Stromal cell- derived factor 1 receptor / SDF-1 receptor / Fusin / Leukocyte-derived seven transmembrane domain receptor / LESTR / LCR1 / FB22 / NPYRL / HM89 / CD184 antigen


Mass: 4518.772 Da / Num. of mol.: 2 / Fragment: N-terminus, residues 1-38 / Mutation: C28A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Production host: Escherichia coli (E. coli) / Strain (production host): SD13009[pREP4] / References: UniProt: P61073

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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)
1413D 13C-F1-filtered 13C-F3-separateded NOESY
1523D 15N-separated NOESY
1623D 13C-separated NOESY
1723D 13C-separated NOESY (AROMATIC)
1823D 13C-F1-filtered 13C-F3-separateded NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1.31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.31 mMCXCL12/SDF1-alpha[U-100% 13C; U-100% 15N]1
.775 mMCXCR41
1.0 mMCXCR4[U-100% 13C; U-100% 15N]2
0.625 mMCXCL12/SDF1-alpha2
Sample conditionsIonic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 308 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.
Software ordinal: 1
Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2012 NOE CONSTRAINTS ( 744 INTRA, 384 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), ...Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2012 NOE CONSTRAINTS ( 744 INTRA, 384 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 92 INTERMOLECULAR CONSTRAINTS (CXCL12 TO CXCR4)) AND 128 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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