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- PDB-1v7m: Human Thrombopoietin Functional Domain Complexed To Neutralizing ... -

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Basic information

Entry
Database: PDB / ID: 1v7m
TitleHuman Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab
Components
  • Monoclonal TN1 Fab Heavy Chain
  • Monoclonal TN1 Fab Light Chain
  • Thrombopoietin
KeywordsIMMUNE SYSTEM/CYTOKINE / Thrombopoietin / Fab fragment / Complex (Cytokine-Antibody) / IMMUNE SYSTEM-CYTOKINE COMPLEX
Function / homology
Function and homology information


thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / megakaryocyte development / Platelet Aggregation (Plug Formation) / cytokine activity / growth factor activity / hormone activity ...thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / megakaryocyte development / Platelet Aggregation (Plug Formation) / cytokine activity / growth factor activity / hormone activity / cell population proliferation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Thrombopoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle ...Thrombopoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsFeese, M.D. / Tamada, T. / Kato, Y. / Maeda, Y. / Hirose, M. / Matsukura, Y. / Shigematsu, H. / Kato, T. / Miyazaki, H. / Kuroki, R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of the receptor-binding domain of human thrombopoietin determined by complexation with a neutralizing antibody fragment
Authors: Feese, M.D. / Tamada, T. / Kato, Y. / Maeda, Y. / Hirose, M. / Matsukura, Y. / Shigematsu, H. / Muto, T. / Matsumoto, A. / Watarai, H. / Ogami, K. / Tahara, T. / Kato, T. / Miyazaki, H. / Kuroki, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization of the Functional Domain of Human Thrombopoietin Using an Antigen-Binding Fragment Derived from Neutralizing Monoclonal Antibody
Authors: Kuroki, R. / Hirose, M. / Kato, Y. / Feese, M.D. / Tamada, T. / Shigematsu, H. / Watarai, H. / Maeda, Y. / Tahara, T. / Kato, T. / Miyazaki, H.
History
DepositionDec 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
L: Monoclonal TN1 Fab Light Chain
H: Monoclonal TN1 Fab Heavy Chain
V: Thrombopoietin
M: Monoclonal TN1 Fab Light Chain
I: Monoclonal TN1 Fab Heavy Chain
X: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)128,3676
Polymers128,3676
Non-polymers00
Water2,810156
1
L: Monoclonal TN1 Fab Light Chain
H: Monoclonal TN1 Fab Heavy Chain
V: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)64,1833
Polymers64,1833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Monoclonal TN1 Fab Light Chain
I: Monoclonal TN1 Fab Heavy Chain
X: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)64,1833
Polymers64,1833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.099, 46.771, 185.151
Angle α, β, γ (deg.)90.00, 90.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Monoclonal TN1 Fab Light Chain


Mass: 23362.854 Da / Num. of mol.: 2 / Fragment: Fab Light Chain
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)
#2: Antibody Monoclonal TN1 Fab Heavy Chain


Mass: 23364.170 Da / Num. of mol.: 2 / Fragment: Fab Heavy Chain
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: Protein Thrombopoietin / Megakaryocyte colony stimulating factor / Myeloproliferative leukemia virus oncogene ligand / C-mpl ...Megakaryocyte colony stimulating factor / Myeloproliferative leukemia virus oncogene ligand / C-mpl ligand / ML / Megakaryocyte growth and development factor / MGDF


Mass: 17456.473 Da / Num. of mol.: 2 / Fragment: TPO Functional Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P40225
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.29 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 0.1M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 295 K / pH: 7 / Method: vapor diffusion, hanging drop
Details: Kuroki, R., (2002) Acta Crystallogr.,Sect.D, 58, 856.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118-20 mg/mlprotein1drop
220 mMimidazole1droppH7.0
319-21 %(w/v)PEG33501reservoir
4100 mMpotassium phosphate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 7, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 36766 / % possible obs: 92 % / Observed criterion σ(I): -1 / Redundancy: 2.6 % / Biso Wilson estimate: 48.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 2814 / Rsym value: 0.318 / % possible all: 71
Reflection
*PLUS
Num. measured all: 120117 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 71 % / Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAI

1iai


Resolution: 2.51→45.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.711 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31579 1852 5 %RANDOM
Rwork0.22751 ---
obs0.23185 34911 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.48 Å2
2--0.05 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 0 156 8902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0218960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.95612192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93751142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.23853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8711.55712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63529240
X-RAY DIFFRACTIONr_scbond_it2.34333248
X-RAY DIFFRACTIONr_scangle_it3.7674.52952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.506→2.571 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 99
Rwork0.27 2010
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / Rfactor Rwork: 0.283

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