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- PDB-7rco: Crystal structure of human TGF-beta-2 bound to 4A11.V2 Fab -

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Basic information

Entry
Database: PDB / ID: 7rco
TitleCrystal structure of human TGF-beta-2 bound to 4A11.V2 Fab
Components
  • 4A11.V2 Fab Heavy Chain
  • 4A11.V2 Fab Light Chain
  • Transforming growth factor beta-2
KeywordsIMMUNE SYSTEM / TGF-beta-2 / Conformational antibody
Function / homology
Function and homology information


regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / positive regulation of heart contraction ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / positive regulation of heart contraction / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / signaling / secondary palate development / glial cell migration / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / atrial septum primum morphogenesis / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / neural retina development / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / negative regulation of Ras protein signal transduction / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / dopamine biosynthetic process / odontogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / hair follicle morphogenesis / generation of neurons / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / activation of protein kinase activity / positive regulation of epithelial cell migration / TGF-beta receptor signaling activates SMADs / uterus development / positive regulation of SMAD protein signal transduction / inner ear development / positive regulation of cell division / hemopoiesis / hair follicle development / ECM proteoglycans / neuron development / epithelial to mesenchymal transition / positive regulation of cell cycle / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / heart morphogenesis / extrinsic apoptotic signaling pathway / epithelial cell differentiation / negative regulation of angiogenesis / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / kidney development / skeletal system development / neural tube closure / cytokine activity / response to progesterone / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / positive regulation of miRNA transcription / response to wounding / negative regulation of epithelial cell proliferation / male gonad development / positive regulation of immune response / positive regulation of neuron apoptotic process / cell migration / Platelet degranulation / heart development / amyloid-beta binding / regulation of cell population proliferation / positive regulation of cell growth / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia
Similarity search - Function
Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...Transforming growth factor beta-2 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYin, J. / Lupardus, P.J. / Sudhamsu, J.
CitationJournal: Sci Rep / Year: 2021
Title: Dramatic activation of an antibody by a single amino acid change in framework.
Authors: Liang, W.C. / Yin, J. / Lupardus, P. / Zhang, J. / Loyet, K.M. / Sudhamsu, J. / Wu, Y.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming growth factor beta-2
B: Transforming growth factor beta-2
C: 4A11.V2 Fab Light Chain
D: 4A11.V2 Fab Heavy Chain
E: 4A11.V2 Fab Light Chain
F: 4A11.V2 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)121,3806
Polymers121,3806
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.154, 103.479, 196.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Transforming growth factor beta-2 / Cetermin / Glioblastoma-derived T-cell suppressor factor / G-TSF / TGF-beta-2


Mass: 12732.597 Da / Num. of mol.: 2 / Fragment: mature domain (UNP residues 303-414)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61812
#2: Antibody 4A11.V2 Fab Light Chain


Mass: 23567.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 4A11.V2 Fab Heavy Chain


Mass: 24389.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 0.1 M sodium cacodylate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→49.06 Å / Num. obs: 27630 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 78.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.048 / Rrim(I) all: 0.099 / Net I/σ(I): 11.6 / Num. measured all: 111744 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.084.30.7311890544290.6630.3890.8311.999.7
8.7-49.063.30.033356110740.9980.0210.03929.593.1

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_finalrefinement
Aimless0.5.28data scaling
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TFG

1tfg


Resolution: 2.9→45.951 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1335 4.84 %
Rwork0.2082 26247 -
obs0.2119 27582 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.34 Å2 / Biso mean: 77.5052 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→45.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 0 48 8200
Biso mean---64.9 -
Num. residues----1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138369
X-RAY DIFFRACTIONf_angle_d1.22911398
X-RAY DIFFRACTIONf_chiral_restr0.0591261
X-RAY DIFFRACTIONf_plane_restr0.0071455
X-RAY DIFFRACTIONf_dihedral_angle_d6.0254945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.00370.34721230.31962630100
3.0037-3.12390.30551140.28852603100
3.1239-3.2660.35871580.26192569100
3.266-3.43820.32571350.25282623100
3.4382-3.65350.36971290.2398263699
3.6535-3.93540.32281260.2208261699
3.9354-4.33120.28231490.193262199
4.3312-4.95730.27321270.1692262298
4.9573-6.24320.2691330.191262597
6.2432-45.9510.2271410.1852270295

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