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- PDB-4kxz: crystal structure of tgfb2 in complex with GC2008. -

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Basic information

Entry
Database: PDB / ID: 4kxz
Titlecrystal structure of tgfb2 in complex with GC2008.
Components
  • GC1008 Heavy Chain
  • GC1008 Light Chain
  • Transforming growth factor beta-2
KeywordsIMMUNE SYSTEM / Cysteine knot / Fab / Various growth functions (TGF-beta) / TGF-beta antagonist (GC2008) / TGF-beta receptors
Function / homology
Function and homology information


regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / regulation of transforming growth factor beta2 production / membranous septum morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of heart contraction / atrial septum morphogenesis / pharyngeal arch artery 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 / TGFBR3 regulates TGF-beta signaling / endocardial cushion fusion / atrial septum primum morphogenesis / positive regulation of integrin biosynthetic process / heart valve morphogenesis / cardiac epithelial to mesenchymal transition / eye development / outflow tract septum morphogenesis / embryonic digestive tract development / positive regulation of stress-activated MAPK cascade / cranial skeletal system development / transforming growth factor beta receptor binding / neural retina development / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / negative regulation of Ras protein signal transduction / odontogenesis / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryo development ending in birth or egg hatching / embryonic limb morphogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / dopamine biosynthetic process / cardiac muscle cell proliferation / hair follicle morphogenesis / endocardial cushion morphogenesis / activation of protein kinase activity / ventricular septum morphogenesis / generation of neurons / positive regulation of Notch signaling pathway / positive regulation of epithelial cell migration / TGF-beta receptor signaling activates SMADs / uterus development / positive regulation of cell division / positive regulation of SMAD protein signal transduction / inner ear development / hemopoiesis / epithelial to mesenchymal transition / hair follicle development / ECM proteoglycans / neuron development / positive regulation of cell cycle / salivary gland morphogenesis / heart morphogenesis / positive regulation of epithelial to mesenchymal transition / epithelial cell differentiation / extrinsic apoptotic signaling pathway / neutrophil chemotaxis / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / kidney development / platelet alpha granule lumen / 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 / positive regulation of neuron apoptotic process / male gonad development / negative regulation of epithelial cell proliferation / positive regulation of immune response / 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
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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMathieu, M. / Moulin, A.G. / Wei, R.
CitationJournal: Protein Sci. / Year: 2014
Title: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions.
Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / ...Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / Bird, J. / Qiu, H. / Pan, C.Q. / Edmunds, T. / Wei, R.R.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transforming growth factor beta-2
B: Transforming growth factor beta-2
D: Transforming growth factor beta-2
E: Transforming growth factor beta-2
H: GC1008 Heavy Chain
J: GC1008 Heavy Chain
N: GC1008 Heavy Chain
Q: GC1008 Heavy Chain
I: GC1008 Light Chain
L: GC1008 Light Chain
M: GC1008 Light Chain
P: GC1008 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,64018
Polymers240,26512
Non-polymers1,3756
Water4,071226
1
A: Transforming growth factor beta-2
B: Transforming growth factor beta-2
H: GC1008 Heavy Chain
J: GC1008 Heavy Chain
I: GC1008 Light Chain
L: GC1008 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5238
Polymers120,1336
Non-polymers3902
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-100 kcal/mol
Surface area46970 Å2
MethodPISA
2
D: Transforming growth factor beta-2
E: Transforming growth factor beta-2
N: GC1008 Heavy Chain
Q: GC1008 Heavy Chain
M: GC1008 Light Chain
P: GC1008 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11710
Polymers120,1336
Non-polymers9844
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-93 kcal/mol
Surface area47730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.200, 359.680, 64.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABDE

#1: Protein
Transforming growth factor beta-2 / TGF-beta-2 / BSC-1 cell growth inhibitor / Cetermin / Glioblastoma-derived T-cell suppressor factor ...TGF-beta-2 / BSC-1 cell growth inhibitor / Cetermin / Glioblastoma-derived T-cell suppressor factor / G-TSF / Polyergin / Latency-associated peptide / LAP


Mass: 12732.597 Da / Num. of mol.: 4 / Fragment: unp residues 303-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61812

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Antibody , 2 types, 8 molecules HJNQILMP

#2: Antibody
GC1008 Heavy Chain


Mass: 23907.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody
GC1008 Light Chain


Mass: 23425.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 232 molecules

#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6
Details: 35% PEG400, 100mM MES, VAPOR DIFFUSION, temperature 296K, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.83→48.73 Å / Num. all: 74556 / Num. obs: 74205 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 68.63 Å2 / Rmerge(I) obs: 0.121
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.83-30.703311829197.3
3-3.20.4045.34111811100
3.2-3.460.2488.35104021100
3.46-3.790.15612.8496311100
3.79-4.230.11217.3887211100
4.23-4.880.07923.3677821100
5.96-8.370.07424.0452241100
8.37-48.730.05232.173158199

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MxCuBEGUIdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→48.73 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9069 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.841 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3709 5 %RANDOM
Rwork0.183 ---
obs-74174 99.87 %-
Displacement parametersBiso max: 149.82 Å2 / Biso mean: 51.0971 Å2 / Biso min: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.5523 Å20 Å20 Å2
2---1.3933 Å20 Å2
3----1.159 Å2
Refine analyzeLuzzati coordinate error obs: 0.334 Å
Refinement stepCycle: LAST / Resolution: 2.83→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16652 0 73 226 16951
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5667SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes354HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2489HARMONIC5
X-RAY DIFFRACTIONt_it17149HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2271SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18537SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17149HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg23361HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion19.06
LS refinement shellResolution: 2.83→2.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3115 266 5 %
Rwork0.2272 5053 -
all0.2313 5319 -
obs--99.87 %

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