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- PDB-1pdg: CRYSTAL STRUCTURE OF HUMAN PLATELET-DERIVED GROWTH FACTOR BB -

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Basic information

Entry
Database: PDB / ID: 1pdg
TitleCRYSTAL STRUCTURE OF HUMAN PLATELET-DERIVED GROWTH FACTOR BB
ComponentsPLATELET-DERIVED GROWTH FACTOR BB
KeywordsGROWTH FACTOR
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 / positive regulation of glomerular filtration / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / cellular response to mycophenolic acid / superoxide-generating NADPH oxidase activator activity / negative regulation of vascular associated smooth muscle cell differentiation ...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 / positive regulation of glomerular filtration / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / cellular response to mycophenolic acid / superoxide-generating NADPH oxidase activator activity / negative regulation of vascular associated smooth muscle cell differentiation / protein kinase C signaling / positive regulation of hyaluronan biosynthetic process / platelet-derived growth factor binding / 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 / monocyte chemotaxis / 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 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 / positive regulation of mitotic nuclear division / negative regulation of miRNA transcription / platelet alpha granule lumen / negative regulation of protein binding / positive regulation of smooth muscle cell proliferation / growth factor activity / positive regulation of MAP kinase activity / cellular response to growth factor stimulus / response to wounding / positive regulation of miRNA transcription / Golgi lumen / peptidyl-tyrosine phosphorylation / 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 / RAF/MAP kinase cascade / basolateral plasma membrane / collagen-containing extracellular matrix / 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 cell migration / protein heterodimerization activity / endoplasmic reticulum lumen / Golgi membrane / protein phosphorylation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...Platelet-derived growth factor, N-terminal / Platelet-derived growth factor, N terminal region / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Platelet-derived growth factor subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsOefner, C. / Darcy, A.D. / Winkler, F.K. / Eggimann, B. / Hosnag, M.
CitationJournal: EMBO J. / Year: 1992
Title: Crystal structure of human platelet-derived growth factor BB.
Authors: Oefner, C. / D'Arcy, A. / Winkler, F.K. / Eggimann, B. / Hosang, M.
History
DepositionJul 14, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLATELET-DERIVED GROWTH FACTOR BB
B: PLATELET-DERIVED GROWTH FACTOR BB
C: PLATELET-DERIVED GROWTH FACTOR BB


Theoretical massNumber of molelcules
Total (without water)36,9413
Polymers36,9413
Non-polymers00
Water0
1
A: PLATELET-DERIVED GROWTH FACTOR BB
B: PLATELET-DERIVED GROWTH FACTOR BB


Theoretical massNumber of molelcules
Total (without water)24,6272
Polymers24,6272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-14 kcal/mol
Surface area11930 Å2
MethodPISA
2
C: PLATELET-DERIVED GROWTH FACTOR BB

C: PLATELET-DERIVED GROWTH FACTOR BB


Theoretical massNumber of molelcules
Total (without water)24,6272
Polymers24,6272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)147.300, 31.800, 90.100
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 41 / 2: CIS PROLINE - PRO B 41 / 3: CIS PROLINE - PRO C 41
DetailsCHAINS A AND B FORM A NON-CRYSTALLOGRAPHIC DISULFIDE LINKED DIMER. CHAIN C IS PART OF A CRYSTALLOGRAPHIC DISULFIDE LINKED DIMER. THE FOLLOWING MATRIX OPERATOR CAN BE USED TO GENERATE THE TWO FOLD RELATED MONOMER FOR THE C CHAIN: -1 0 0 0 1 0 0 0 -1

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Components

#1: Protein PLATELET-DERIVED GROWTH FACTOR BB


Mass: 12313.501 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01127

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
225 %isopropanol1reservoir
325 %PEG4001reservoir
4250 mM1reservoirCaCl2
520 mMHEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 8544 / % possible obs: 99 % / Num. measured all: 24377 / Rmerge(I) obs: 0.061

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.209 6172
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 0 0 2037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d2.5
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / Num. reflection obs: 6172 / σ(F): 3 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.5

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