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- PDB-3mjg: The structure of a platelet derived growth factor receptor complex -

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Basic information

Entry
Database: PDB / ID: 3mjg
TitleThe structure of a platelet derived growth factor receptor complex
Components
  • Beta-type platelet-derived growth factor receptor
  • Platelet-derived growth factor subunit B
KeywordsHormone/Transferase / protein-protein complex / growth factor-receptor complex / Transferase-Hormone complex / Hormone-Transferase complex
Function / homology
Function and homology information


metanephric glomerular mesangial cell development / positive regulation of vascular associated smooth muscle cell dedifferentiation / platelet-derived growth factor complex / positive regulation of metanephric mesenchymal cell migration / negative regulation of phosphatidylinositol biosynthetic process / platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development ...metanephric glomerular mesangial cell development / positive regulation of vascular associated smooth muscle cell dedifferentiation / platelet-derived growth factor complex / positive regulation of metanephric mesenchymal cell migration / negative regulation of phosphatidylinositol biosynthetic process / platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of glomerular filtration / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cellular response to mycophenolic acid / superoxide-generating NADPH oxidase activator activity / negative regulation of vascular associated smooth muscle cell differentiation / cell migration involved in vasculogenesis / protein kinase C signaling / aorta morphogenesis / positive regulation of hyaluronan biosynthetic process / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / retina vasculature development in camera-type eye / vascular endothelial growth factor binding / cardiac myofibril assembly / phosphatidylinositol metabolic process / positive regulation of glomerular mesangial cell proliferation / positive regulation of chemotaxis / interleukin-18-mediated signaling pathway / Signaling by PDGF / paracrine signaling / platelet-derived growth factor receptor binding / positive regulation of vascular associated smooth muscle cell migration / positive regulation of cell-substrate adhesion / positive regulation of DNA biosynthetic process / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / positive regulation of calcium ion import / chemoattractant activity / platelet-derived growth factor receptor-beta signaling pathway / monocyte chemotaxis / positive regulation of phosphoprotein phosphatase activity / positive regulation of cell division / platelet-derived growth factor receptor signaling pathway / Non-integrin membrane-ECM interactions / negative regulation of platelet activation / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / positive regulation of phospholipase C activity / positive regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / reactive oxygen species metabolic process / positive regulation of endothelial cell proliferation / cell chemotaxis / Downstream signal transduction / lysosomal lumen / positive regulation of mitotic nuclear division / negative regulation of miRNA transcription / platelet alpha granule lumen / negative regulation of protein binding / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / growth factor activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / cellular response to growth factor stimulus / response to wounding / positive regulation of miRNA transcription / Golgi lumen / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT signaling / gene expression / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / basolateral plasma membrane / protein tyrosine kinase activity / collagen-containing extracellular matrix / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / protein kinase activity / positive regulation of cell migration / apical plasma membrane / protein heterodimerization activity / endoplasmic reticulum lumen / Golgi membrane / protein phosphorylation
Similarity search - Function
Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / Platelet-derived growth factor receptor beta / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site ...Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / Platelet-derived growth factor receptor beta / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Platelet-derived growth factor subunit B / Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShim, A.H.R. / He, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex.
Authors: Shim, A.H. / Liu, H. / Focia, P.J. / Chen, X. / Lin, P.C. / He, X.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-derived growth factor subunit B
B: Platelet-derived growth factor subunit B
X: Beta-type platelet-derived growth factor receptor
Y: Beta-type platelet-derived growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,27618
Polymers104,1794
Non-polymers3,09714
Water21,0781170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: Beta-type platelet-derived growth factor receptor
hetero molecules

A: Platelet-derived growth factor subunit B
B: Platelet-derived growth factor subunit B
X: Beta-type platelet-derived growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,27618
Polymers104,1794
Non-polymers3,09714
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_545-x+1/2,-y-1,z+1/21
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint3 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.470, 116.820, 134.150
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-derived growth factor subunit B / / PDGF subunit B / Platelet-derived growth factor B chain / Platelet-derived growth factor beta ...PDGF subunit B / Platelet-derived growth factor B chain / Platelet-derived growth factor beta polypeptide / PDGF-2 / Proto-oncogene c-Sis


Mass: 19596.301 Da / Num. of mol.: 2 / Fragment: UNP residues 21-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGF2, PDGFB, SIS / Cell line (production host): Embryonic Kidney-293 cells / Production host: Homo sapiens / References: UniProt: P01127
#2: Protein Beta-type platelet-derived growth factor receptor / PDGF-R-beta / CD140 antigen-like family member B


Mass: 32493.354 Da / Num. of mol.: 2 / Fragment: UNP residues 33-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFRB / Cell line (production host): Embryonic Kidney-293 cells / Production host: Homo sapiens
References: UniProt: P09619, receptor protein-tyrosine kinase
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1170 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.84 M (NH4)2HPO4, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→44.24 Å / Num. all: 55432 / Num. obs: 54767 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.3 / Num. unique all: 8466 / Rsym value: 0.426 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1pdg, 1flt

1pdg

1flt


Resolution: 2.3→44.24 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2835260.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2764 5.1 %RANDOM
Rwork0.237 ---
obs0.237 54642 98.9 %-
all-55249 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.54 Å2 / ksol: 0.272531 e/Å3
Displacement parametersBiso mean: 67.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.52 Å20 Å20 Å2
2--11.67 Å20 Å2
3----6.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 196 1170 7254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d1.19
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 439 4.9 %
Rwork0.338 8466 -
obs-8466 97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4ion.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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