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- PDB-2k05: Structure of SDF1 in complex with the CXCR4 N-terminus containing... -

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Basic information

Entry
Database: PDB / ID: 2k05
TitleStructure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21
Components
  • C-X-C chemokine receptor type 4
  • Stromal cell-derived factor 1
KeywordsCYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / CXCR4 / chemokine / sulfotyrosine / 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 / positive regulation of axon extension involved in axon guidance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of vasculature development / Signaling by ROBO receptors / induction of positive chemotaxis / negative regulation of dendritic cell apoptotic process / Formation of definitive endoderm / integrin activation / positive regulation of dopamine secretion / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to chemokine / C-C chemokine receptor activity / C-C chemokine binding / positive regulation of monocyte chemotaxis / anchoring junction / chemokine activity / Chemokine receptors bind chemokines / dendritic cell chemotaxis / blood circulation / positive regulation of calcium ion import / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / cell leading edge / positive regulation of oligodendrocyte differentiation / animal organ regeneration / Binding and entry of HIV virion / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of T cell migration / Nuclear signaling by ERBB4 / regulation of cell adhesion / coreceptor activity / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / neurogenesis / positive regulation of cell adhesion / axon guidance / chemokine-mediated signaling pathway / growth factor activity / cell chemotaxis / adult locomotory behavior / ubiquitin binding / calcium-mediated signaling / defense response / brain development / response to peptide hormone / integrin binding / G protein-coupled receptor activity / neuron migration / response to virus / chemotaxis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / late endosome / positive regulation of cold-induced thermogenesis / virus receptor activity / extracellular matrix / positive regulation of cytosolic calcium ion concentration / actin binding / cytoplasmic vesicle / Estrogen-dependent gene expression / G alpha (i) signalling events / response to hypoxia / early endosome / lysosome / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / 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 1.2Feb 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_struct_assembly / pdbx_struct_oper_list / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 6, 2024Group: Database references / Structure summary
Category: 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
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)25,8954
Polymers25,8954
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): SG13009[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: 4758.960 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): SG13009[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
1.338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .97 mM CXCR4, 90% H2O, 10% D2O90% H2O/10% D2O
21.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.338 mMCXCL12/SDF1-alpha[U-100% 13C; U-100% 15N]1
.97 mMCXCR41
1.07 mMCXCR4[U-100% 13C; U-100% 15N]2
0.67 mMCXCL12/SDF1-alpha2
Sample conditionsIonic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 308 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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
XwinNMR3.5Brukercollection
X-PLOR NIH2.9.3Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3Bartels et al.data analysis
SPSCAN1.1.0Glaserpeak picking
GARANT2.1Bartels, Guntert, Billeter and Wuthrichchemical shift assignment
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 2092 NOE CONSTRAINTS (722 INTRA, 566 SEQUENTIAL, 238 MEDIUM, 420 LONG RANGE, 116 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), ...Details: CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2092 NOE CONSTRAINTS (722 INTRA, 566 SEQUENTIAL, 238 MEDIUM, 420 LONG RANGE, 116 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 86 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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