[English] 日本語
Yorodumi
- PDB-8dc0: Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dc0
TitleRat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R)
Components
  • Transforming growth factor beta receptor type 3
  • Transforming growth factor beta-2
KeywordsCYTOKINE / Complex / Betaglycan / TGFb2
Function / homology
Function and homology information


TGFBR3 PTM regulation / TGFBR3 regulates FGF2 signaling / negative regulation of apoptotic process involved in morphogenesis / TGFBR3 regulates activin signaling / response to luteinizing hormone / transforming growth factor beta receptor activity, type III / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / transforming growth factor beta receptor complex assembly / epicardium-derived cardiac fibroblast cell development ...TGFBR3 PTM regulation / TGFBR3 regulates FGF2 signaling / negative regulation of apoptotic process involved in morphogenesis / TGFBR3 regulates activin signaling / response to luteinizing hormone / transforming growth factor beta receptor activity, type III / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / transforming growth factor beta receptor complex assembly / epicardium-derived cardiac fibroblast cell development / Signaling by BMP / TGF-beta receptor signaling activates SMADs / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / inhibin-betaglycan-ActRII complex / ascending aorta morphogenesis / positive regulation of activation-induced cell death of T cells / cardioblast differentiation / response to follicle-stimulating hormone / muscular septum morphogenesis / uterine wall breakdown / definitive erythrocyte differentiation / positive regulation of timing of catagen / TGFBR3 regulates TGF-beta signaling / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / regulation of transforming growth factor beta2 production / BMP binding / atrial septum morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of heart contraction / Signaling by Activin / apoptotic process involved in morphogenesis / transforming growth factor beta receptor activity / activation-induced cell death of T cells / glial cell migration / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of extracellular matrix disassembly / secondary palate development / negative regulation of macrophage cytokine production / negative regulation of epithelial cell migration / somatic stem cell division / positive regulation of integrin biosynthetic process / endocardial cushion fusion / atrial septum primum morphogenesis / ventricular compact myocardium morphogenesis / heart valve morphogenesis / membranous septum morphogenesis / negative regulation of cartilage development / cardiac epithelial to mesenchymal transition / TGFBR3 regulates TGF-beta signaling / signaling / positive regulation of stress-activated MAPK cascade / neuron fate commitment / pericyte cell differentiation / collagen metabolic process / transforming growth factor beta receptor binding / eye development / embryonic digestive tract development / neural retina development / type II transforming growth factor beta receptor binding / activin binding / cranial skeletal system development / heart trabecula morphogenesis / pulmonary valve morphogenesis / glycosaminoglycan binding / ventricular trabecula myocardium morphogenesis / negative regulation of Ras protein signal transduction / positive regulation of BMP signaling pathway / embryo development ending in birth or egg hatching / outflow tract septum morphogenesis / heart trabecula formation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / definitive hemopoiesis / cell-cell junction organization / transforming growth factor beta binding / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / atrioventricular valve morphogenesis / face morphogenesis / negative regulation of extracellular matrix assembly / odontogenesis / positive regulation of cell migration involved in sprouting angiogenesis / Molecules associated with elastic fibres / negative regulation of epithelial to mesenchymal transition / endocardial cushion morphogenesis / hair follicle morphogenesis / cartilage condensation / dopamine biosynthetic process / ventricular cardiac muscle tissue morphogenesis / generation of neurons / ventricular septum morphogenesis / blood vessel development / positive regulation of Notch signaling pathway
Similarity search - Function
Transforming growth factor beta-2 proprotein / : / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain ...Transforming growth factor beta-2 proprotein / : / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / 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 receptor type 3 / Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWieteska, L. / Taylor, A.B. / Hinck, A.P.
Funding support United States, European Union, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058067 United States
H2020 Marie Curie Actions of the European Commission893196European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structures of TGF-β with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling.
Authors: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando ...Authors: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando López-Casillas / Peter Cherepanov / Daniel J Bernard / Caroline S Hill / Andrew P Hinck /
Abstract: Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility ...Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.
History
DepositionJun 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming growth factor beta receptor type 3
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)32,8612
Polymers32,8612
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-4 kcal/mol
Surface area14510 Å2
Unit cell
Length a, b, c (Å)76.456, 90.453, 98.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-221-

HOH

-
Components

#1: Protein Transforming growth factor beta receptor type 3 / TGF-beta receptor type 3 / TGFR-3 / Betaglycan / Transforming growth factor beta receptor III / TGF- ...TGF-beta receptor type 3 / TGFR-3 / Betaglycan / Transforming growth factor beta receptor III / TGF-beta receptor type III


Mass: 19915.881 Da / Num. of mol.: 1 / Fragment: ZPC domain (UNP residues 590-757)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tgfbr3 / Production host: Homo sapiens (human) / References: UniProt: P26342
#2: Protein Transforming growth factor beta-2 / mmTGF-b2-7m2r / TGF-beta-2


Mass: 12944.903 Da / Num. of mol.: 1 / Fragment: mmTGF-b2-7m2r (UNP residues 303-414)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61812
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 13% PEG4000, 0.1 M trisodium citrate, 10% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→66.74 Å / Num. obs: 26131 / % possible obs: 99.84 % / Redundancy: 13 % / Biso Wilson estimate: 38.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1789 / Rrim(I) all: 0.1863 / Net I/σ(I): 9.27
Reflection shellResolution: 1.93→1.999 Å / Num. unique obs: 2560 / CC1/2: 0.404

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3QW9 & 5TX4

3qw9

5tx4


Resolution: 1.93→66.74 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2566 1998 7.65 %
Rwork0.2186 24109 -
obs0.2215 26107 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.87 Å2
Refinement stepCycle: LAST / Resolution: 1.93→66.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 0 85 2131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062098
X-RAY DIFFRACTIONf_angle_d0.91512842
X-RAY DIFFRACTIONf_chiral_restr0.0805314
X-RAY DIFFRACTIONf_plane_restr0.0065361
X-RAY DIFFRACTIONf_dihedral_angle_d15.1793777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.44941400.3921697X-RAY DIFFRACTION99.57
1.98-2.030.39721410.35871688X-RAY DIFFRACTION99.95
2.03-2.090.34531400.3171696X-RAY DIFFRACTION99.84
2.09-2.160.35741410.29191704X-RAY DIFFRACTION99.89
2.16-2.240.29471420.27111695X-RAY DIFFRACTION100
2.24-2.330.30171420.27551715X-RAY DIFFRACTION100
2.33-2.430.31921400.25421694X-RAY DIFFRACTION99.89
2.43-2.560.31171430.23621722X-RAY DIFFRACTION99.79
2.56-2.720.2711420.23891717X-RAY DIFFRACTION99.95
2.72-2.930.27071430.22491722X-RAY DIFFRACTION99.79
2.93-3.220.29121430.22331727X-RAY DIFFRACTION99.79
3.23-3.690.22381440.19451742X-RAY DIFFRACTION99.84
3.69-4.650.22451440.17771734X-RAY DIFFRACTION99.84
4.65-66.740.21111530.19641856X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.651377602630.775698668992.037325574781.416710623351.573484066192.61421878682-0.0722482236788-0.07125738008110.03842829334260.0749252379779-0.2051726237030.2647370367480.0605534540059-0.651314556550.2892578601590.35984298441-0.02681445503510.09134589955780.574517641757-0.07692133225710.47385760965413.378317323613.924613236718.7429458582
23.916836963461.455036593380.5185677107744.353055659181.381619628132.844835628730.0725066219699-0.3087989724390.139511573670.193461115156-0.151461278612-0.0376182515246-0.0620945216971-0.09924618096540.07949244622390.2430246984620.007094168050040.01263830617040.371364671119-0.02113710899820.28333026517725.849378663816.595363919215.8847059418
32.22096628677-0.805898796325-2.22340058615.147110691235.852171216797.456645191450.2229258514360.874658561019-1.086184767320.114701883782-0.3349765359761.507404375961.162547188660.5195240268460.3995696766470.8600993989030.114734270734-0.1392114363661.13322130632-0.007076001178331.0524350830516.04682888725.453613211531.1594842002
45.164126451660.4871427284321.186956541766.379034440083.607929905023.50470450255-0.0852052229527-0.3259585202340.2215307976340.123332254114-0.3589237449010.2876734759820.0190270151911-0.4389960070530.4100971580680.217666332029-0.01913588114190.02231261560460.5410432898430.0287695942360.30521344368118.534610106615.5523897511.2838721011
54.668719336075.707130703396.069009498667.931174088846.665496416628.82108373932-0.0827073467156-0.2773919663510.6682553996420.349990266336-0.05293366257450.1577088615490.0390367999688-0.135646217667-0.07269351548840.2648909750860.01609378502320.008955718476620.428811785632-0.09309309002830.31144373899627.332984674412.379339826517.5810929952
64.51064344798-1.62614199836-1.199590375536.56155880941-0.7678450264376.36016838569-0.00258175231729-0.7247201993850.3387566710790.3115236569010.07334134098880.0198704864414-0.1949076383050.468879339986-0.04008107224030.276480204599-0.0497471192009-0.008455843833990.503599695168-0.2179494098750.47950137748338.032895677323.902891919122.5644739285
79.434909958165.347931902555.032717486187.887691187386.080526138858.82047242780.318474578679-0.328509653782-0.326456829861-0.114730609965-0.3523311241920.3125985679830.224355165711-1.091035931940.1620544058340.3498499887320.009520704201570.1226127951410.267637576319-0.01535762686260.28880104307618.07962428848.7968853424712.1830402379
85.41584499289-1.705377760951.931364030622.448375618-0.8120741318129.014751558750.0856274960518-0.3876489740720.278980892187-0.128980485989-0.159581929848-0.7141811058780.1459217777220.7340333104290.09680583566580.3380389329170.0109614213522-0.02186751048660.4562038764450.05906651356880.47083252545467.74947045883.242059563839.44613817965
99.47569886834-6.538435663941.137070576584.60406787312-0.7393687457360.880630589644-0.0638444746684-0.347167754807-1.33553533426-0.02814564912850.1719522783481.099997985880.312605730617-0.246755679298-0.1544418372580.3648082399420.0045224422160.03565053040580.4301782256360.02131255412950.45130466867943.19641040519.843605451568.10256557045
103.08416891856-1.17677652392-1.951066190666.27442782410.4490695621281.28212456617-0.088477580533-0.03814902037450.2240492698270.802567533681-0.0869733727759-0.194426801758-0.2200865289560.5952526100260.2593338937470.370513153071-0.0398584318791-0.001609193734450.4042778087430.03958638010890.33721676182162.79258002914.917339722616.9389070858
116.59437148286-6.330160287416.448146332536.12581897104-6.194897091916.26092419483-0.0457166994254-0.4886476829830.395570231245-0.2379065912470.48812265540.105021008794-0.169621709480.264679949163-0.6411519095930.546123536520.0732508823844-0.07973551458030.73767575887-0.1568930811640.54371745334662.316977021912.12153710216.6179240534
124.60583905685-6.1005999006-1.440977397669.340463319530.8447199749744.965777747530.3703219521060.8595081804471.745260421820.357663574064-0.388275330915-0.5001820975690.0264922908765-0.02458301031960.09096922879550.3648732580560.02193717074230.01264248886830.3127025922580.0165603023910.40354195819341.62975656922.8109129616.74508534945
139.9739010171-5.445188670865.69920682629.48956991559-5.488310180526.68353713507-0.715141148225-0.8446374984340.4869620249760.691182953520.156166246975-0.642946365392-0.28596305974-0.1363369711650.6545886234170.4373190951880.0045696232209-0.082054572120.570462845818-0.1205316121650.49867894077161.382089260112.40361963115.0007578934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 41 )AA15 - 411 - 27
22chain 'A' and (resid 42 through 93 )AA42 - 9328 - 79
33chain 'A' and (resid 94 through 107 )AA94 - 10780 - 93
44chain 'A' and (resid 108 through 123 )AA108 - 12394 - 109
55chain 'A' and (resid 124 through 135 )AA124 - 135110 - 121
66chain 'A' and (resid 136 through 167 )AA136 - 167122 - 153
77chain 'A' and (resid 168 through 181 )AA168 - 181154 - 167
88chain 'B' and (resid 1 through 20 )BB1 - 201 - 20
99chain 'B' and (resid 21 through 37 )BB21 - 3721 - 37
1010chain 'B' and (resid 38 through 76 )BB38 - 7638 - 52
1111chain 'B' and (resid 77 through 85 )BB77 - 8553 - 61
1212chain 'B' and (resid 86 through 101 )BB86 - 10162 - 77
1313chain 'B' and (resid 102 through 112 )BB102 - 11278 - 88

+
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