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- PDB-1v7n: Human Thrombopoietin Functional Domain Complexed To Neutralizing ... -

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Basic information

Entry
Database: PDB / ID: 1v7n
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


positive regulation of hematopoietic stem cell proliferation / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / thrombopoietin-mediated signaling pathway / cell surface receptor signaling pathway via STAT / megakaryocyte development / Platelet Aggregation (Plug Formation) / cytokine activity / growth factor activity / hormone activity ...positive regulation of hematopoietic stem cell proliferation / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / thrombopoietin-mediated signaling pathway / cell surface receptor signaling pathway via STAT / megakaryocyte development / Platelet Aggregation (Plug Formation) / cytokine activity / growth factor activity / hormone activity / positive regulation of protein phosphorylation / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / 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: 3.3 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
M: Monoclonal TN1 Fab Light Chain
I: Monoclonal TN1 Fab Heavy Chain
N: Monoclonal TN1 Fab Light Chain
J: Monoclonal TN1 Fab Heavy Chain
O: Monoclonal TN1 Fab Light Chain
K: Monoclonal TN1 Fab Heavy Chain
V: Thrombopoietin
X: Thrombopoietin
Y: Thrombopoietin
Z: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)256,85012
Polymers256,85012
Non-polymers00
Water3,045169
1
L: Monoclonal TN1 Fab Light Chain
H: Monoclonal TN1 Fab Heavy Chain
V: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)64,2133
Polymers64,2133
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)64,2133
Polymers64,2133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
N: Monoclonal TN1 Fab Light Chain
J: Monoclonal TN1 Fab Heavy Chain
Y: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)64,2133
Polymers64,2133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: Monoclonal TN1 Fab Light Chain
K: Monoclonal TN1 Fab Heavy Chain
Z: Thrombopoietin


Theoretical massNumber of molelcules
Total (without water)64,2133
Polymers64,2133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.038, 46.582, 191.359
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Monoclonal TN1 Fab Light Chain


Mass: 23362.854 Da / Num. of mol.: 4 / 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.: 4 / 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: 17485.539 Da / Num. of mol.: 4 / Fragment: TPO Functional Domain / Mutation: Q115R
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.: 169 / 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: 2.42 Å3/Da / Density % sol: 48.88 %
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: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 1, 1998
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→60 Å / Num. obs: 35598 / % possible obs: 98 % / Observed criterion σ(I): -0.5 / Redundancy: 1.6 % / Biso Wilson estimate: 36.6 Å2 / Rsym value: 0.098 / Net I/σ(I): 3
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 3468 / Rsym value: 0.214 / % possible all: 97
Reflection
*PLUS
Num. measured all: 74809 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.214

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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: 3.3→57.63 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.77 / SU B: 34.656 / SU ML: 0.581 / Cross valid method: THROUGHOUT / ESU R Free: 0.737 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30477 1801 5 %RANDOM
Rwork0.16708 ---
obs0.17405 34015 98.45 %-
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: 29.767 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-0.33 Å2
2--2.25 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 3.3→57.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17297 0 0 169 17466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02117722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7681.95424136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.13352266
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_restr0.1730.22752
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213236
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3370.210891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.21057
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3290.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.511334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.934218321
X-RAY DIFFRACTIONr_scbond_it2.82736388
X-RAY DIFFRACTIONr_scangle_it4.7774.55815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 125
Rwork0.183 2479
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.028
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.374 / Rfactor Rwork: 0.181

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