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- PDB-2nwg: Structure of CXCL12:heparin disaccharide complex -

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Basic information

Entry
Database: PDB / ID: 2nwg
TitleStructure of CXCL12:heparin disaccharide complex
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE / SIGNALING PROTEIN / protein-glycosaminoglycan complex
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
Stromal cell-derived factor 1 / CXC Chemokine domain / 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
HEPARIN DISACCHARIDE I-S, / Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMurphy, J.W. / Cho, Y. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Functional Basis of CXCL12 (Stromal Cell-derived Factor-1{alpha}) Binding to Heparin
Authors: Murphy, J.W. / Cho, Y. / Sachpatzidis, A. / Fan, C. / Hodsdon, M.E. / Lolis, E.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Stromal cell-derived factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1444
Polymers15,9892
Non-polymers1,1552
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-28 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.492, 56.965, 71.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsasymmetric consists of a biological dimer

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Components

#1: Protein Stromal cell-derived factor 1 / / CXCL12 / SDF-1 / Pre-B cell growth-stimulating factor / PBSF / hIRH


Mass: 7994.504 Da / Num. of mol.: 2 / Fragment: residues 22-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48061
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose / HEPARIN DISACCHARIDE I-S /


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 577.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with ring modification on monosaccharide components
References: HEPARIN DISACCHARIDE I-S,
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][b-D-4-deoxy-GlcpA2SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: soaking / pH: 8.5
Details: Grown in 2M Ammonium Sulfate, 0.1M TrisHCl pH 8.50. Soaked in 20 mM PEG-8000, 1M TrisHCl pH 8.5, 16 mM disaccharide. , Soaking, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→25.582 Å / Num. obs: 9627 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Χ2: 1.272 / Net I/σ(I): 31.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.07-2.186.50.3672904513850.367100
2.18-2.316.60.2592.8848412870.259100
2.31-2.476.60.1733.9808312290.173100
2.47-2.676.60.1215.8755411400.121100
2.67-2.936.60.0867.9707410660.086100
2.93-3.276.60.0659.364299710.065100
3.27-3.786.60.05510.757448700.055100
3.78-4.636.60.04812.148187350.048100
4.63-6.556.30.04213.137515910.042100
6.55-26.475.80.03415.620353530.03498.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2 Å35.87 Å
Translation2 Å35.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→23.34 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 459 4.8 %RANDOM
Rwork0.24 ---
obs0.241 9589 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.07→23.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 70 50 1207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221184
X-RAY DIFFRACTIONr_angle_refined_deg2.5192.051615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3175130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44923.46252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70615214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.321510
X-RAY DIFFRACTIONr_chiral_restr0.2110.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02836
X-RAY DIFFRACTIONr_nbd_refined0.2570.2475
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.29
X-RAY DIFFRACTIONr_mcbond_it1.371.5667
X-RAY DIFFRACTIONr_mcangle_it2.25521084
X-RAY DIFFRACTIONr_scbond_it1.6543517
X-RAY DIFFRACTIONr_scangle_it2.3734.5531
LS refinement shellResolution: 2.07→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 33 -
Rwork0.292 668 -
obs-701 100 %

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