[English] 日本語
Yorodumi
- PDB-8udz: The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex -

+
Open data


ID or keywords:

Loading...

-
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 / frontal suture morphogenesis / 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 / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development ...cellular response to acetaldehyde / frontal suture morphogenesis / 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 / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development / embryonic liver development / macrophage derived foam cell differentiation / response to laminar fluid shear stress / regulation of branching involved in mammary gland duct 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 / tolerance induction to self antigen / regulation of blood vessel remodeling / regulation of protein import into nucleus / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / myofibroblast differentiation / positive regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / odontoblast differentiation / negative regulation of macrophage cytokine production / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / heart valve morphogenesis / mammary gland branching involved in thelarche / bronchiole development / TGFBR3 regulates TGF-beta signaling / hyaluronan catabolic process / positive regulation of vasculature development / lens fiber cell differentiation / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of chemotaxis / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / positive regulation of mononuclear cell migration / response to salt / germ cell migration / negative regulation of biomineral tissue development / endoderm development / phospholipid homeostasis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / positive regulation of vascular permeability / response to cholesterol / oligodendrocyte development / negative regulation of interleukin-17 production / cell-cell junction organization / phosphate-containing compound metabolic process / surfactant homeostasis / sprouting angiogenesis / deubiquitinase activator activity / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of ossification / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / digestive tract development / RUNX3 regulates CDKN1A transcription / response to vitamin D / face morphogenesis / positive regulation of fibroblast migration / ureteric bud development / neural tube development / positive regulation of regulatory T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / Molecules associated with elastic fibres / negative regulation of phagocytosis / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of neuroblast proliferation / lung alveolus development / Syndecan interactions / ventricular cardiac muscle tissue morphogenesis / muscle cell cellular homeostasis / cellular response to insulin-like growth factor stimulus / negative regulation of fat cell differentiation / odontogenesis of dentin-containing tooth
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more