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- PDB-8udz: The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex -

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Basic information

Entry
Database: PDB / ID: 8udz
TitleThe Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex
Components
  • (LTBP-49247 Fab ...) x 2
  • Transforming growth factor beta-1 proprotein
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Growth factor / antibody / fibrosis / TGFbeta / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


cellular response to acetaldehyde / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis / macrophage derived foam cell differentiation ...cellular response to acetaldehyde / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis / macrophage derived foam cell differentiation / frontal suture morphogenesis / regulation of enamel mineralization / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulatory T cell differentiation / regulation of blood vessel remodeling / tolerance induction to self antigen / regulation of protein import into nucleus / embryonic liver development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / columnar/cuboidal epithelial cell maturation / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / heart valve morphogenesis / retina vasculature development in camera-type eye / TGFBR3 regulates TGF-beta signaling / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / positive regulation of vasculature development / response to laminar fluid shear stress / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / negative regulation of extracellular matrix disassembly / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / type II transforming growth factor beta receptor binding / receptor catabolic process / TGFBR1 LBD Mutants in Cancer / oligodendrocyte development / response to salt / type I transforming growth factor beta receptor binding / germ cell migration / negative regulation of biomineral tissue development / positive regulation of mononuclear cell migration / endoderm development / phospholipid homeostasis / negative regulation of myoblast differentiation / positive regulation of chemotaxis / negative regulation of cell-cell adhesion mediated by cadherin / cell-cell junction organization / response to vitamin D / response to cholesterol / positive regulation of vascular permeability / negative regulation of interleukin-17 production / surfactant homeostasis / deubiquitinase activator activity / phosphate-containing compound metabolic process / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of chemokine (C-X-C motif) ligand 2 production / digestive tract development / positive regulation of fibroblast migration / aortic valve morphogenesis / sprouting angiogenesis / negative regulation of ossification / RUNX3 regulates CDKN1A transcription / face morphogenesis / neural tube development / positive regulation of regulatory T cell differentiation / ureteric bud development / Molecules associated with elastic fibres / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of phagocytosis / negative regulation of neuroblast proliferation / muscle cell cellular homeostasis / cellular response to insulin-like growth factor stimulus / Syndecan interactions / ventricular cardiac muscle tissue morphogenesis / lung alveolus development / negative regulation of fat cell differentiation / positive regulation of interleukin-17 production
Similarity search - Function
Transforming growth factor beta-1 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-1 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-1 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsStreich Jr., F.C. / Nicholls, S.B. / Boston, C.J. / Ramachandran, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Sci.Signal. / Year: 2024
Title: An antibody that inhibits TGF-beta 1 release from latent extracellular matrix complexes attenuates the progression of renal fibrosis.
Authors: Jackson, J.W. / Streich Jr., F.C. / Pal, A. / Coricor, G. / Boston, C. / Brueckner, C.T. / Canonico, K. / Chapron, C. / Cote, S. / Dagbay, K.B. / Danehy Jr., F.T. / Kavosi, M. / Kumar, S. / ...Authors: Jackson, J.W. / Streich Jr., F.C. / Pal, A. / Coricor, G. / Boston, C. / Brueckner, C.T. / Canonico, K. / Chapron, C. / Cote, S. / Dagbay, K.B. / Danehy Jr., F.T. / Kavosi, M. / Kumar, S. / Lin, S. / Littlefield, C. / Looby, K. / Manohar, R. / Martin, C.J. / Wood, M. / Zawadzka, A. / Wawersik, S. / Nicholls, S.B. / Datta, A. / Buckler, A. / Schurpf, T. / Carven, G.J. / Qatanani, M. / Fogel, A.I.
History
DepositionSep 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming growth factor beta-1 proprotein
B: Transforming growth factor beta-1 proprotein
C: LTBP-49247 Fab Heavy Chain
D: LTBP-49247 Fab Light Chain
E: LTBP-49247 Fab Heavy Chain
F: LTBP-49247 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,9659
Polymers179,6126
Non-polymers1,3533
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.495, 141.905, 186.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11F-397-

HOH

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Components

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody LTBP-49247 Fab Heavy Chain


Mass: 25100.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell (production host): EPITHELIAL / Cell line (production host): Expi293F GnTI- Cells / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Strain (production host): Expi293F GnTI- Cells / Tissue (production host): KIDNEY / Variant (production host): GnTI- Cells
#3: Antibody LTBP-49247 Fab Light Chain


Mass: 23484.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell (production host): EPITHELIAL / Cell line (production host): Expi293F GnTI- Cells / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Strain (production host): Expi293F GnTI- Cells / Tissue (production host): KIDNEY / Variant (production host): GnTI- Cells

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Protein / Non-polymers , 2 types, 234 molecules AB

#1: Protein Transforming growth factor beta-1 proprotein


Mass: 41221.035 Da / Num. of mol.: 2 / Mutation: C33S, R278A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Plasmid: pTT5 / Cell (production host): EPITHELIAL / Cell line (production host): Expi293F GnTI- Cells / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Strain (production host): Expi293F GnTI- Cells / Tissue (production host): KIDNEY / Variant (production host): GnTI- Cells / References: UniProt: P01137
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 15% PEG 3350, 12% Tacsimate (pH 4.0), 10 mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.21→73.5 Å / Num. obs: 98200 / % possible obs: 99.46 % / Redundancy: 13.1 % / Biso Wilson estimate: 62.32 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.103 / Net I/σ(I): 13.3
Reflection shellResolution: 2.21→2.289 Å / Redundancy: 12.9 % / Rmerge(I) obs: 3.364 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 9725 / CC1/2: 0.351 / Rpim(I) all: 0.967 / Rrim(I) all: 3.502 / % possible all: 94.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
PHASER2.8.3phasing
Coot0.9.6model building
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→73.5 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2643 4891 5.01 %
Rwork0.2316 --
obs0.2333 97670 99.46 %
Refinement stepCycle: LAST / Resolution: 2.21→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11003 0 89 232 11324

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