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- PDB-4r9y: Crystal structure of KKOFab in complex with platelet factor 4 -

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Basic information

Entry
Database: PDB / ID: 4r9y
TitleCrystal structure of KKOFab in complex with platelet factor 4
Components
  • Platelet factor 4 antibody KKO heavy chain
  • Platelet factor 4 antibody KKO light chain
  • Platelet factor 4
KeywordsIMMUNE SYSTEM/Cytokine / KKO / PF4 / HIT / immunoglobulin / CXC chemokine / antibody / antigen / blood / IMMUNE SYSTEM-Cytokine complex
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / killing by host of symbiont cells / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / defense response to protozoan / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of megakaryocyte differentiation / Common Pathway of Fibrin Clot Formation / negative regulation of angiogenesis / neutrophil chemotaxis / platelet alpha granule lumen / Cell surface interactions at the vascular wall / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / cytokine-mediated 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 / G alpha (i) signalling events / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / inflammatory response / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.11 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Platelet factor 4
C: Platelet factor 4
L: Platelet factor 4 antibody KKO light chain
H: Platelet factor 4 antibody KKO heavy chain
B: Platelet factor 4
A: Platelet factor 4
M: Platelet factor 4 antibody KKO light chain
N: Platelet factor 4 antibody KKO heavy chain


Theoretical massNumber of molelcules
Total (without water)125,2138
Polymers125,2138
Non-polymers00
Water0
1
D: Platelet factor 4
L: Platelet factor 4 antibody KKO light chain
H: Platelet factor 4 antibody KKO heavy chain
B: Platelet factor 4


Theoretical massNumber of molelcules
Total (without water)62,6064
Polymers62,6064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-43 kcal/mol
Surface area27340 Å2
MethodPISA
2
C: Platelet factor 4
A: Platelet factor 4
M: Platelet factor 4 antibody KKO light chain
N: Platelet factor 4 antibody KKO heavy chain


Theoretical massNumber of molelcules
Total (without water)62,6064
Polymers62,6064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-43 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.490, 99.340, 261.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
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: Antibody Platelet factor 4 antibody KKO light chain


Mass: 23725.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)
#3: Antibody Platelet factor 4 antibody KKO heavy chain


Mass: 23316.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)

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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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7% PEG6000, 0.1 M Tris-HCl, pH7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 29, 2012
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 9343 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
4.1-4.174.50.441161.3
4.17-4.255.60.399168.8
4.25-4.335.70.319168.4
4.33-4.426.40.232170.5
4.42-4.516.60.227175.1
4.51-4.626.80.236177.1

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.11→20 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.786 / SU B: 319.337 / SU ML: 1.901 / Cross valid method: THROUGHOUT / ESU R Free: 1.778 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.38218 419 4.9 %RANDOM
Rwork0.31678 ---
obs0.31985 8063 78.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 267.597 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---1.3 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 4.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8548 0 0 0 8548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_other_d0.0060.028750
X-RAY DIFFRACTIONr_angle_other_deg0.9231.9611918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6251116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.40324.451328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.775151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2771534
X-RAY DIFFRACTIONr_chiral_restr0.0550.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216482
LS refinement shellResolution: 4.11→4.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 5 -
Rwork0.487 89 -
obs--13.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5295-4.25362.609315.87853.898710.59720.78860.10680.4019-1.9095-0.5966-0.95931.0957-0.0681-0.1920.9912-0.0023-0.01010.12610.14920.241348.354-66.36118.4739
24.35520.0927.65193.6606-1.203613.96920.48450.05980.0188-1.0806-0.5651-0.5291.45750.30980.08061.1766-0.03950.08130.1869-0.01530.209250.6806-80.568514.4539
30.9029-0.7242-0.50621.16260.45310.3012-0.8591-0.42520.35310.60241.036-0.3750.50770.2623-0.17691.24090.2956-0.4960.8641-0.12450.759935.6361-20.560624.9465
41.23820.66470.47382.6663-2.8685.8544-0.5588-0.0408-0.3109-0.22561.3080.4164-0.8462-1.1223-0.74910.4678-0.10210.16150.9330.33160.44426.64-31.477413.8443
57.9822-1.77826.446114.5979-4.532910.21840.1864-0.1327-0.76690.22640.4491.1585-0.0191-0.7749-0.63540.0614-0.0555-0.03610.20470.06410.172141.3566-64.803631.0938
66.0523-4.1372-0.473813.769-5.58266.06450.43880.65410.39030.3092-0.9644-0.7116-0.38520.14610.52560.1506-0.09050.06950.34060.05340.209556.7271-65.075431.7313
70.04730.3121-0.10134.9121-1.84542.4399-0.01220.06470.05041.1446-0.2627-0.50180.09540.29730.2750.6339-0.1236-0.2530.30310.28720.307358.5276-100.238559.1135
80.1828-0.4715-0.61241.90220.59775.9913-0.01940.03380.2987-0.5287-0.5156-1.28881.77930.09780.5350.85980.01980.54661.1370.6911.363569.4169-100.591544.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D6 - 70
2X-RAY DIFFRACTION2C6 - 70
3X-RAY DIFFRACTION3L26 - 239
4X-RAY DIFFRACTION4H1 - 218
5X-RAY DIFFRACTION5B6 - 70
6X-RAY DIFFRACTION6A6 - 70
7X-RAY DIFFRACTION7M26 - 239
8X-RAY DIFFRACTION8N1 - 218

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