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- PDB-2n55: Structure of constitutively monomeric CXCL12 in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 2n55
TitleStructure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus
Components
  • C-X-C chemokine receptor type 4
  • Stromal cell-derived factor 1
KeywordsCYTOKINE/Signaling Protein / CXL12 / CXCR4 / chemokine / GPCR / SDF1 / CYTOKINE-Signaling Protein complex
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 / negative regulation of dendritic cell apoptotic process / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway ...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 / negative regulation of dendritic cell apoptotic process / 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 / 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 / positive regulation of calcium ion import / cellular response to cytokine stimulus / 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 / Nuclear signaling by ERBB4 / positive regulation of T cell migration / positive regulation of neuron differentiation / neurogenesis / adult locomotory behavior / coreceptor activity / positive regulation of endothelial cell proliferation / positive regulation of cell adhesion / axon guidance / calcium-mediated signaling / chemokine-mediated signaling pathway / brain development / growth factor activity / cell chemotaxis / ubiquitin binding / neuron migration / defense response / 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 / actin binding / cytoplasmic vesicle / extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / G alpha (i) signalling events / early endosome / 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 / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsZiarek, J.J. / Peterson, F.C. / Volkman, B.F.
CitationJournal: Sci Signal / Year: 2017
Title: Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation.
Authors: Ziarek, J.J. / Kleist, A.B. / London, N. / Raveh, B. / Montpas, N. / Bonneterre, J. / St-Onge, G. / DiCosmo-Ponticello, C.J. / Koplinski, C.A. / Roy, I. / Stephens, B. / Thelen, S. / ...Authors: Ziarek, J.J. / Kleist, A.B. / London, N. / Raveh, B. / Montpas, N. / Bonneterre, J. / St-Onge, G. / DiCosmo-Ponticello, C.J. / Koplinski, C.A. / Roy, I. / Stephens, B. / Thelen, S. / Veldkamp, C.T. / Coffman, F.D. / Cohen, M.C. / Dwinell, M.B. / Thelen, M. / Peterson, F.C. / Heveker, N. / Volkman, B.F.
History
DepositionJul 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3May 3, 2017Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5Oct 9, 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
B: C-X-C chemokine receptor type 4


Theoretical massNumber of molelcules
Total (without water)12,6652
Polymers12,6652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3281.2 Å2
ΔGint-10.4 kcal/mol
Surface area7408.4 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 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B ...SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B cell growth-stimulating factor / PBSF / SDF-1-beta(3-72) / SDF-1-alpha(3-67)


Mass: 8146.680 Da / Num. of mol.: 1 / Mutation: L76C, I79C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P48061
#2: Protein/peptide C-X-C chemokine receptor type 4 / CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain ...CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain receptor / LESTR / Lipopolysaccharide-associated protein 3 / LAP-3 / LPS-associated protein 3 / NPYRL / Stromal cell-derived factor 1 receptor / SDF-1 receptor


Mass: 4518.772 Da / Num. of mol.: 1 / Mutation: C28A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / 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 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1423D 1H-15N NOESY
1523D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1713D F1-13C filtered/F3-13C edited NOESY aliphatic
1823D F1-13C filtered/F3-13C edited NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-99% 13C; U-99% 15N]1
25 mMMES-2[U-2H]1
10 %D2O-3[U-99% 2H]1
0.02 %sodium azide-41
2 mMentity_2-51
1 mMentity_2-6[U-99% 13C; U-99% 15N]2
25 mMMES-7[U-2H]2
0.02 %sodium azide-82
10 %D2O-9[U-99% 2H]2
2 mMentity_1-102
Sample conditionsIonic strength: 0.02 / 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1533 / NOE intraresidue total count: 365 / NOE long range total count: 486 / NOE medium range total count: 241 / NOE sequential total count: 441 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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