[English] 日本語
Yorodumi
- EMDB-19111: CryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19111
TitleCryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.
Map dataMain map: Sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model refinement. Additional map: DeepEMhancer sharpened map, used for model building and map visualization.
Sample
  • Complex: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: mFab LMT-12, Light Chain
    • Protein or peptide: mFab LMT-12, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1 proprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGARP / TGF-B1 / ACTIVATION / TREG / IMMUNE SYSTEM / ANTIBODY
Function / homology
Function and homology information


regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Syndecan interactions / TGFBR3 regulates TGF-beta signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Molecules associated with elastic fibres / establishment of protein localization to extracellular region / leukocyte proliferation / connective tissue development ...regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Syndecan interactions / TGFBR3 regulates TGF-beta signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Molecules associated with elastic fibres / establishment of protein localization to extracellular region / leukocyte proliferation / connective tissue development / TGF-beta receptor signaling activates SMADs / cellular response to acetaldehyde / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / frontal suture morphogenesis / regulation of enamel mineralization / regulation of cartilage development / regulation of striated muscle tissue development / regulatory T cell differentiation / tolerance induction to self antigen / Regulation of RUNX3 expression and activity / 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 / odontoblast differentiation / positive regulation of odontogenesis / Langerhans cell differentiation / negative regulation of macrophage cytokine production / positive regulation of smooth muscle cell differentiation / mononuclear cell proliferation / positive regulation of exit from mitosis / regulation of regulatory T cell differentiation / secondary palate development / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / Cell surface interactions at the vascular wall / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / retina vasculature development in camera-type eye / heart valve morphogenesis / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / positive regulation of vasculature development / response to laminar fluid shear stress / Platelet degranulation / negative regulation of T cell activation / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / type II transforming growth factor beta receptor binding / receptor catabolic process / cell activation / oligodendrocyte development / receptor ligand inhibitor activity / 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 / mammary gland development / response to vitamin D / cell-cell junction organization / response to cholesterol / positive regulation of vascular permeability / negative regulation of interleukin-17 production / surfactant homeostasis / deubiquitinase activator activity / phosphate-containing compound metabolic process / transforming growth factor beta binding / negative regulation of release of sequestered calcium ion into cytosol / digestive tract development / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of fibroblast migration / aortic valve morphogenesis / negative regulation of ossification / face morphogenesis / sprouting angiogenesis / neural tube development / positive regulation of regulatory T cell differentiation
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. / Leucine rich repeat, ribonuclease inhibitor type / Leucine-rich repeats, bacterial type / Cystine-knot cytokine / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Transforming growth factor beta activator LRRC32 / Transforming growth factor beta-1 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFelix J / Lambert F / Marien L / van der Woning B / Savvides SN / Lucas S
Funding support Belgium, 5 items
OrganizationGrant numberCountry
Other privateFondation contre le Cancer / 2020-079
Other governmentARC / 19/24-098
Fonds National de la Recherche Scientifique (FNRS)PDR / T.0145.21 Belgium
Fonds National de la Recherche Scientifique (FNRS)WELBIO / CR2019A-02R Belgium
Other privateSalus Sanguinis
CitationJournal: To Be Published
Title: TGF-beta1 activating antibodies as novel immunotherapeutics for graft-versus-host disease.
Authors: Lambert F / Felix J / Wautier S / Gaignage M / Dupre E / Marien L / Lesage M / van der Woning B / Coulie PG / Savvides SN / Lucas S
History
DepositionDec 12, 2023-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19111.png

Downloads & links

-
Map

FileDownload / File: emd_19111.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map: Sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model refinement. Additional map: DeepEMhancer sharpened map, used for model building and map visualization.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3829911 - 0.6301
Average (Standard dev.)0.00006955558 (±0.009160325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19111_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: DeepEMhancer sharpened map of mouse GARP-lTGFbeta1 in complex...

Fileemd_19111_additional_1.map
AnnotationDeepEMhancer sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model building and map visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.

Fileemd_19111_half_map_1.map
AnnotationHalf map 2 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.

Fileemd_19111_half_map_2.map
AnnotationHalf map 1 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.

EntireName: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
Components
  • Complex: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: mFab LMT-12, Light Chain
    • Protein or peptide: mFab LMT-12, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1 proprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.

SupramoleculeName: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 259.9 KDa

-
Macromolecule #1: Transforming growth factor beta-1 proprotein

MacromoleculeName: Transforming growth factor beta-1 proprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.369926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPSGLRLLP LLLPLPWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESADPEPEP EADYYAKEVT RVLMVDRNNA IYEKTKDISH SIYMFFNTSD IREAVPEPPL LSRAELRLQR L KSSVEQHV ...String:
MPPSGLRLLP LLLPLPWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESADPEPEP EADYYAKEVT RVLMVDRNNA IYEKTKDISH SIYMFFNTSD IREAVPEPPL LSRAELRLQR L KSSVEQHV ELYQKYSNNS WRYLGNRLLT PTDTPEWLSF DVTGVVRQWL NQGDGIQGFR FSAHCSCDSK DNKLHVEING IS PKRRGDL GTIHDMNRPF LLLMATPLER AQHLHSSRHR RALDTNYCFS STEKNCCVRQ LYIDFRKDLG WKWIHEPKGY HAN FCLGPC PYIWSLDTQY SKVLALYNQH NPGASASPCC VPQALEPLPI VYYVGRKPKV EQLSNMIVRS CKCS

UniProtKB: Transforming growth factor beta-1 proprotein

-
Macromolecule #2: Transforming growth factor beta activator LRRC32

MacromoleculeName: Transforming growth factor beta activator LRRC32 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 73.699914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSHQILLLLA MLTLGLAISQ RREQVPCRTV NKEALCHGLG LLQVPSVLSL DIQALYLSGN QLQSILVSPL GFYTALRHLD LSDNQISFL QAGVFQALPY LEHLNLAHNR LATGMALNSG GLGRLPLLVS LDLSGNSLHG NLVERLLGET PRLRTLSLAE N SLTRLARH ...String:
MSHQILLLLA MLTLGLAISQ RREQVPCRTV NKEALCHGLG LLQVPSVLSL DIQALYLSGN QLQSILVSPL GFYTALRHLD LSDNQISFL QAGVFQALPY LEHLNLAHNR LATGMALNSG GLGRLPLLVS LDLSGNSLHG NLVERLLGET PRLRTLSLAE N SLTRLARH TFWGMPAVEQ LDLHSNVLMD IEDGAFEALP HLTHLNLSRN SLTCISDFSL QQLQVLDLSC NSIEAFQTAP EP QAQFQLA WLDLRENKLL HFPDLAVFPR LIYLNVSNNL IQLPAGLPRG SEDLHAPSEG WSASPLSNPS RNASTHPLSQ LLN LDLSYN EIELVPASFL EHLTSLRFLN LSRNCLRSFE ARQVDSLPCL VLLDLSHNVL EALELGTKVL GSLQTLLLQD NALQ ELPPY TFASLASLQR LNLQGNQVSP CGGPAEPGPP GCVDFSGIPT LHVLNMAGNS MGMLRAGSFL HTPLTELDLS TNPGL DVAT GALVGLEASL EVLELQGNGL TVLRVDLPCF LRLKRLNLAE NQLSHLPAWT RAVSLEVLDL RNNSFSLLPG NAMGGL ETS LRRLYLQGNP LSCCGNGWLA AQLHQGRVDV DATQDLICRF GSQEELSLSL VRPEDCEKGG LKNVNLEAAA ENLYFQG AA WSHPQFEKGA AWSHPQFEKG AAWSHPQFEK GAA

UniProtKB: Transforming growth factor beta activator LRRC32

-
Macromolecule #3: mFab LMT-12, Light Chain

MacromoleculeName: mFab LMT-12, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.713555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ PALTQLSSMS GSPGQTVTIT CTGSSSNIGG GYYLNWYQQL PGAAPKLVIY NANNRASGVP DRFSGSKSG NLASLTITGL QAEDEAVYFC GCYDSSLSSV VFGGGTHLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL I SDFYPGAV ...String:
MGWSCIILFL VATATGVHSQ PALTQLSSMS GSPGQTVTIT CTGSSSNIGG GYYLNWYQQL PGAAPKLVIY NANNRASGVP DRFSGSKSG NLASLTITGL QAEDEAVYFC GCYDSSLSSV VFGGGTHLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL I SDFYPGAV TVAWKADSSP VKAGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

-
Macromolecule #4: mFab LMT-12, Heavy Chain

MacromoleculeName: mFab LMT-12, Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.143363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YYMYWVRQAP GKGLEWVSGT SIGGGSTWYA DSVKGRFTI SRDNAKNTLY LQMNNLKSED TAVYYCAKDL NSRSYKGMGD WGQGTQVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YYMYWVRQAP GKGLEWVSGT SIGGGSTWYA DSVKGRFTI SRDNAKNTLY LQMNNLKSED TAVYYCAKDL NSRSYKGMGD WGQGTQVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP KSCDKTH

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1
Details: Grids were acquired via PUXANO (https://puxano.com)
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13898 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Details: A total of 6605 untilted movies were collected followed by 3508 movies at 20 degree tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Alphafold models of mouse GARP and mouse transforming growth factor beta 1 pro-protein
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 288887
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

9-f1

source_name: AlphaFold, initial_model_type: in silico model

2-f1

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8rex:
CryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.

+
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