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- PDB-6p7j: Crystal structure of Latency Associated Peptide unbound to TGF-beta1 -

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Basic information

Entry
Database: PDB / ID: 6p7j
TitleCrystal structure of Latency Associated Peptide unbound to TGF-beta1
ComponentsTransforming growth factor beta-1 proprotein
KeywordsCYTOKINE / pro-domain / latency / cancer / transforming
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 / molecular replacement / Resolution: 3.501 Å
AuthorsStachowski, T.R. / Snell, M.E. / Snell, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Iucrj / Year: 2020
Title: Structural insights into conformational switching in latency-associated peptide between transforming growth factor beta-1 bound and unbound states
Authors: Stachowski, T.R. / Snell, M.E. / Snell, E.H.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming growth factor beta-1 proprotein


Theoretical massNumber of molelcules
Total (without water)29,2741
Polymers29,2741
Non-polymers00
Water00
1
A: Transforming growth factor beta-1 proprotein

A: Transforming growth factor beta-1 proprotein


Theoretical massNumber of molelcules
Total (without water)58,5482
Polymers58,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area2230 Å2
ΔGint-1 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 154.900, 62.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Transforming growth factor beta-1 proprotein


Mass: 29274.240 Da / Num. of mol.: 1 / Mutation: R249A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Plasmid: pTT3 / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01137
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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.6
Details: Reservoir composition: 20% PEG3350, 300 mM NaAc pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→36.31 Å / Num. obs: 3332 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.899 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.209 / Rrim(I) all: 0.406 / Net I/σ(I): 3.1 / Num. measured all: 12411 / Scaling rejects: 46
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
3.5-3.833.51.6926687730.4671.1062.0341.199.5
8.57-36.313.90.0769862560.9880.0420.0876.798.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
MR-Rosettaphasing
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VQP

5vqp


Resolution: 3.501→36.31 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.3215 160 4.81 %
Rwork0.2881 --
obs0.2897 3329 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 224.46 Å2 / Biso mean: 111.1007 Å2 / Biso min: 40.77 Å2
Refinement stepCycle: final / Resolution: 3.501→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 0 0 1298
Num. residues----159
LS refinement shellResolution: 3.501→3.625 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3315 12 -
Rwork0.3296 324 -
obs--99 %

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