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- PDB-4qci: PDGF-B blocking antibody bound to PDGF-BB -

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Basic information

Entry
Database: PDB / ID: 4qci
TitlePDGF-B blocking antibody bound to PDGF-BB
Components
  • Platelet-derived growth factor subunit B
  • anti-PDGF-BB antibody - Heavy chain
  • anti-PDGF-BB antibody - Light Chain
KeywordsCYTOKINE/CYTOKINE RECEPTOR / growth factor cytokine fold / growth factor hormone / PDGFR-beta receptor / extracellular / CYTOKINE-CYTOKINE RECEPTOR 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet-derived growth factor subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKuai, J. / Mosyak, L. / Tam, M. / LaVallie, E. / Pullen, N. / Carven, G.
CitationJournal: Biochemistry / Year: 2015
Title: Characterization of Binding Mode of Action of a Blocking Anti-Platelet-Derived Growth Factor (PDGF)-B Monoclonal Antibody, MOR8457, Reveals Conformational Flexibility and Avidity Needed for ...Title: Characterization of Binding Mode of Action of a Blocking Anti-Platelet-Derived Growth Factor (PDGF)-B Monoclonal Antibody, MOR8457, Reveals Conformational Flexibility and Avidity Needed for PDGF-BB To Bind PDGF Receptor-beta.
Authors: Kuai, J. / Mosyak, L. / Brooks, J. / Cain, M. / Carven, G.J. / Ogawa, S. / Ishino, T. / Tam, M. / Lavallie, E.R. / Yang, Z. / Ponsel, D. / Rauchenberger, R. / Arch, R. / Pullen, N.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / 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 / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-PDGF-BB antibody - Light Chain
B: anti-PDGF-BB antibody - Heavy chain
C: Platelet-derived growth factor subunit B
D: Platelet-derived growth factor subunit B
H: anti-PDGF-BB antibody - Heavy chain
L: anti-PDGF-BB antibody - Light Chain


Theoretical massNumber of molelcules
Total (without water)117,4166
Polymers117,4166
Non-polymers00
Water5,891327
1
A: anti-PDGF-BB antibody - Light Chain
B: anti-PDGF-BB antibody - Heavy chain
D: Platelet-derived growth factor subunit B


Theoretical massNumber of molelcules
Total (without water)58,7083
Polymers58,7083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-31 kcal/mol
Surface area25070 Å2
MethodPISA
2
C: Platelet-derived growth factor subunit B
H: anti-PDGF-BB antibody - Heavy chain
L: anti-PDGF-BB antibody - Light Chain


Theoretical massNumber of molelcules
Total (without water)58,7083
Polymers58,7083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-35 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.150, 68.470, 95.250
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-PDGF-BB antibody - Light Chain


Mass: 22382.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody anti-PDGF-BB antibody - Heavy chain


Mass: 23880.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: 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: 12444.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDGFB, PDGF2, SIS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01127
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18 C from a solution containing 22% PEG 3350 and 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→69.64 Å / Num. all: 51112 / Num. obs: 51112 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Biso Wilson estimate: 62.06 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.11.1refinement
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→69.64 Å / Cor.coef. Fo:Fc: 0.9302 / Cor.coef. Fo:Fc free: 0.9004 / SU R Cruickshank DPI: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 2612 5.11 %RANDOM 5%
Rwork0.2112 ---
obs0.213 51112 99.4 %-
all-51112 --
Displacement parametersBiso mean: 65.25 Å2
Baniso -1Baniso -2Baniso -3
1-6.104 Å20 Å2-8.8531 Å2
2---9.4643 Å20 Å2
3---3.3603 Å2
Refine analyzeLuzzati coordinate error obs: 0.342 Å
Refinement stepCycle: LAST / Resolution: 2.3→69.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 0 327 8086
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097960HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1910857HARMONIC2
X-RAY DIFFRACTIONc_dihedral_angle_d22626SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes51154HARMONIC5
X-RAY DIFFRACTIONc_mcangle_it07960HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion17.93
X-RAY DIFFRACTIONt_chiral_improper_torsion51067SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact48594SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2632 187 5.06 %
Rwork0.2412 3512 -
all0.2423 3699 -
obs--99.4 %

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