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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


telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / C-X-C motif chemokine 12 receptor activity / response to ultrasound / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells ...telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / C-X-C motif chemokine 12 receptor activity / response to ultrasound / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells / chemokine receptor binding / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development / induction of positive chemotaxis / Signaling by ROBO receptors / negative regulation of dendritic cell apoptotic process / Formation of definitive endoderm / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / integrin activation / positive regulation of dopamine secretion / cellular response to chemokine / C-C chemokine binding / C-C chemokine receptor activity / positive regulation of monocyte chemotaxis / anchoring junction / chemokine activity / Chemokine receptors bind chemokines / blood circulation / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / cellular response to cytokine stimulus / positive regulation of calcium ion import / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / animal organ regeneration / Binding and entry of HIV virion / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / positive regulation of T cell migration / Nuclear signaling by ERBB4 / adult locomotory behavior / neurogenesis / coreceptor activity / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / positive regulation of cell adhesion / axon guidance / calcium-mediated signaling / chemokine-mediated signaling pathway / growth factor activity / brain development / cell chemotaxis / ubiquitin binding / defense response / neuron migration / response to virus / intracellular calcium ion homeostasis / integrin binding / response to peptide hormone / chemotaxis / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / late endosome / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / virus receptor activity / extracellular matrix / actin binding / cytoplasmic vesicle / Estrogen-dependent gene expression / G alpha (i) signalling events / early endosome / response to hypoxia / lysosome / cell adhesion / immune response / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / ubiquitin protein ligase binding / apoptotic process / cell surface / signal transduction / protein-containing complex / : / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CXC Chemokine domain / Chemokine receptor family / 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 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CXC Chemokine domain / Chemokine receptor family / 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) / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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
Revision 1.6Nov 27, 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

Downloads & links

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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
Water00
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
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)
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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