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- PDB-4hqu: Crystal structure of human PDGF-BB in complex with a modified nuc... -

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Basic information

Entry
Database: PDB / ID: 4hqu
TitleCrystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5)
Components
  • Platelet-derived growth factor subunit B
  • SOMAmer SL5
KeywordsHORMONE/DNA / Growth factor / SELEX / aptamer / 5-modified deoxyuridine / HORMONE-DNA 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 / 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
DNA / DNA (> 10) / Platelet-derived growth factor subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavies, D.R. / Edwards, T.E. / Janjic, N. / Gelinas, A.D. / Zhang, C. / Jarvis, T.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.
Authors: Davies, D.R. / Gelinas, A.D. / Zhang, C. / Rohloff, J.C. / Carter, J.D. / O'Connell, D. / Waugh, S.M. / Wolk, S.K. / Mayfield, W.S. / Burgin, A.B. / Edwards, T.E. / Stewart, L.J. / Gold, L. ...Authors: Davies, D.R. / Gelinas, A.D. / Zhang, C. / Rohloff, J.C. / Carter, J.D. / O'Connell, D. / Waugh, S.M. / Wolk, S.K. / Mayfield, W.S. / Burgin, A.B. / Edwards, T.E. / Stewart, L.J. / Gold, L. / Janjic, N. / Jarvis, T.C.
History
DepositionOct 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: SOMAmer SL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9254
Polymers20,8772
Non-polymers472
Water1,47782
1
A: Platelet-derived growth factor subunit B
C: SOMAmer SL5
hetero molecules

A: Platelet-derived growth factor subunit B
C: SOMAmer SL5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8508
Polymers41,7554
Non-polymers954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10160 Å2
ΔGint-12 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.710, 59.710, 167.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-102-

MG

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Components

#1: Protein Platelet-derived growth factor subunit B / / PDGF subunit B / PDGF-2 / Platelet-derived growth factor B chain / Platelet-derived growth factor ...PDGF subunit B / PDGF-2 / Platelet-derived growth factor B chain / Platelet-derived growth factor beta polypeptide / Proto-oncogene c-Sis


Mass: 12313.501 Da / Num. of mol.: 1 / Fragment: PDGF-BB, UNP residues 82-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFB, PDGF2, SIS / Production host: Escherichia coli (E. coli) / References: UniProt: P01127
#2: DNA chain SOMAmer SL5


Mass: 8563.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized oligonucleotide
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROPLEX D8: 0.1 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 15% PEG 6000, VAPOR DIFFUSION, TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979176 / Wavelength: 0.979176 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.2→19.27 Å / Num. obs: 15629 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.44 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.33
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A of 3MJG

3mjg


Resolution: 2.2→19.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.589 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF
RfactorNum. reflection% reflectionSelection details
Rfree0.262 786 5 %RANDOM
Rwork0.225 ---
obs0.227 15628 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2--1.88 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 556 2 82 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0181381
X-RAY DIFFRACTIONr_angle_refined_deg1.8822.1361973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.751596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73922.81332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82115135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.888159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021893
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 51 -
Rwork0.329 954 -
obs--98.82 %

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