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- PDB-4r9w: Crystal structure of platelet factor 4 complexed with fondaparinux -

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Basic information

Entry
Database: PDB / ID: 4r9w
TitleCrystal structure of platelet factor 4 complexed with fondaparinux
ComponentsPlatelet factor 4
KeywordsCYTOKINE / PF4 / fondaparinux / CXC chemokine / platelet factor / glycosaminoglycan / platelet
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / killing by host of symbiont cells / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / leukocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / defense response to protozoan ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / killing by host of symbiont cells / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / leukocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / defense response to protozoan / monocyte chemotaxis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of blood coagulation / negative regulation of megakaryocyte differentiation / Common Pathway of Fibrin Clot Formation / neutrophil chemotaxis / negative regulation of angiogenesis / platelet alpha granule lumen / Cell surface interactions at the vascular wall / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cytokine-mediated signaling pathway / platelet activation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / : / G alpha (i) signalling events / inflammatory response / receptor ligand activity / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
fondaparinux / Platelet factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.
CitationJournal: Nat Commun / Year: 2015
Title: Atomic description of the immune complex involved in heparin-induced thrombocytopenia.
Authors: Cai, Z. / Yarovoi, S.V. / Zhu, Z. / Rauova, L. / Hayes, V. / Lebedeva, T. / Liu, Q. / Poncz, M. / Arepally, G. / Cines, D.B. / Greene, M.I.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jul 12, 2017Group: Structure summary / Item: _chem_comp.pdbx_synonyms
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Platelet factor 4
B: Platelet factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0733
Polymers15,5642
Non-polymers1,5081
Water30617
1
A: Platelet factor 4
B: Platelet factor 4
hetero molecules

A: Platelet factor 4
B: Platelet factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1456
Polymers31,1294
Non-polymers3,0172
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6500 Å2
ΔGint-35 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.333, 67.333, 61.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Platelet factor 4 / PF-4 / C-X-C motif chemokine 4 / Iroplact / Oncostatin-A / Platelet factor 4 / short form


Mass: 7782.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PF4, CXCL4, SCYB4 / Cell line (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P02776
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside / fondaparinux


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1508.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: fondaparinux
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2% PEG4000, 17% MPD, 0.1 M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 5900 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.545.30.689198.2
2.54-2.595.60.492197.8
2.59-2.645.70.478199.4
2.64-2.695.80.462199
2.69-2.755.80.411100
2.75-2.825.80.25199.3

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→22.756 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 32.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 256 4.46 %
Rwork0.2235 --
obs0.2244 5742 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→22.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 91 17 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061083
X-RAY DIFFRACTIONf_angle_d0.9281478
X-RAY DIFFRACTIONf_dihedral_angle_d25.54452
X-RAY DIFFRACTIONf_chiral_restr0.532202
X-RAY DIFFRACTIONf_plane_restr0.004163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.14890.33311250.34092715X-RAY DIFFRACTION99
3.1489-22.7570.22611310.20252771X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 17.4423 Å / Origin y: 20.9149 Å / Origin z: 8.2694 Å
111213212223313233
T0.3722 Å2-0.0072 Å2-0.0627 Å2-0.6502 Å20.0908 Å2--0.4423 Å2
L4.9819 °2-0.4018 °21.1796 °2-5.9353 °20.2278 °2--3.7957 °2
S0.2163 Å °-1.0576 Å °-0.4224 Å °0.432 Å °0.1495 Å °-0.2469 Å °0.274 Å °0.1713 Å °0.0657 Å °
Refinement TLS groupSelection details: all

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