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- PDB-8v52: Crystal structure of 2A10 Fab bound to Human TGF-beta3 -

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Basic information

Entry
Database: PDB / ID: 8v52
TitleCrystal structure of 2A10 Fab bound to Human TGF-beta3
Components
  • 2A10 Fab Heavy Chain
  • 2A10 Fab Light chain
  • Transforming growth factor beta-3
KeywordsCYTOKINE/IMMUNE SYSTEM / TGF beta / 2A10 / complex / fab / CYTOKINE / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding ...frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization / digestive tract development / transforming growth factor beta binding / face morphogenesis / odontogenesis / Molecules associated with elastic fibres / positive regulation of filopodium assembly / lung alveolus development / TGF-beta receptor signaling activates SMADs / inner ear development / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of SMAD protein signal transduction / positive regulation of cell division / ECM proteoglycans / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / positive regulation of stress fiber assembly / T-tubule / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / female pregnancy / cytokine activity / positive regulation of protein secretion / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / response to estrogen / Platelet degranulation / regulation of cell population proliferation / collagen-containing extracellular matrix / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / response to hypoxia / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Transforming growth factor beta-3 / 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-3 / 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-3 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYin, J. / Lupardus, P.J.
Funding support1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD
CitationJournal: Med / Year: 2024
Title: Isoform-selective TGF-beta 3 inhibition for systemic sclerosis.
Authors: Sun, T. / Vander Heiden, J.A. / Gao, X. / Yin, J. / Uttarwar, S. / Liang, W.C. / Jia, G. / Yadav, R. / Huang, Z. / Mitra, M. / Halpern, W. / Bender, H.S. / Brightbill, H.D. / Wu, Y. / ...Authors: Sun, T. / Vander Heiden, J.A. / Gao, X. / Yin, J. / Uttarwar, S. / Liang, W.C. / Jia, G. / Yadav, R. / Huang, Z. / Mitra, M. / Halpern, W. / Bender, H.S. / Brightbill, H.D. / Wu, Y. / Lupardus, P. / Ramalingam, T. / Arron, J.R.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor beta-3
B: Transforming growth factor beta-3
C: 2A10 Fab Light chain
D: 2A10 Fab Heavy Chain
E: 2A10 Fab Light chain
F: 2A10 Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)121,4346
Polymers121,4346
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.940, 47.200, 200.830
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Transforming growth factor beta-3 / / TGF-beta-3


Mass: 12734.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB3 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10600
#2: Antibody 2A10 Fab Light chain


Mass: 23881.557 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 2A10 Fab Heavy Chain


Mass: 24100.832 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 / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 25% PEG 1000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→49.17 Å / Num. obs: 75332 / % possible obs: 97.2 % / Redundancy: 5.6 % / CC1/2: 0.996 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 3072 / CC1/2: 0.514

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.17 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.464 / SU Rfree Blow DPI: 0.285 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2096 4.88 %RANDOM
Rwork0.221 ---
obs0.223 42938 99.2 %-
Displacement parametersBiso mean: 60.49 Å2
Baniso -1Baniso -2Baniso -3
1--5.9995 Å20 Å2-7.316 Å2
2--3.8694 Å20 Å2
3---2.1301 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.5→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7869 0 0 161 8030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018072HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2211015HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2605SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1347HARMONIC5
X-RAY DIFFRACTIONt_it8072HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion19.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1070SEMIHARMONIC5
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_contact8903SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3214 131 4.26 %
Rwork0.2394 2941 -
all0.2428 3072 -
obs--97.9 %

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