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- PDB-8dc0: Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini m... -

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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


TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex ...TGF-beta receptor signaling activates SMADs / negative regulation of apoptotic process involved in morphogenesis / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / response to luteinizing hormone / epicardium-derived cardiac fibroblast cell development / transforming growth factor beta receptor activity, type III / Signaling by BMP / transforming growth factor beta receptor complex assembly / inhibin-betaglycan-ActRII complex / regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / muscular septum morphogenesis / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / definitive erythrocyte differentiation / positive regulation of timing of catagen / response to follicle-stimulating hormone / positive regulation of cardioblast differentiation / positive regulation of heart contraction / response to prostaglandin E / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / BMP binding / atrial septum morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / Signaling by Activin / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / apoptotic process involved in morphogenesis / signaling / transforming growth factor beta receptor activity / secondary palate development / ventricular compact myocardium morphogenesis / glial cell migration / somatic stem cell division / negative regulation of epithelial cell migration / heart valve morphogenesis / endocardial cushion fusion / atrial septum primum morphogenesis / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / collagen metabolic process / regulation of transforming growth factor beta receptor signaling pathway / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / neural retina development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / heart trabecula morphogenesis / activin binding / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / heart trabecula formation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / negative regulation of Ras protein signal transduction / transforming growth factor beta binding / negative regulation of epithelial to mesenchymal transition / definitive hemopoiesis / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / negative regulation of extracellular matrix assembly / embryo development ending in birth or egg hatching / odontogenesis / dopamine biosynthetic process / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / hair follicle morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / generation of neurons / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / negative regulation of SMAD protein signal transduction / activation of protein kinase activity / roof of mouth development / positive regulation of epithelial cell migration / fibroblast growth factor binding / blood vessel development / positive regulation of transforming growth factor beta receptor signaling pathway / outflow tract morphogenesis / SMAD binding / TGF-beta receptor signaling activates SMADs / uterus development / positive regulation of SMAD protein signal transduction / inner ear development
Similarity search - Function
Transforming growth factor beta-2 proprotein / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Transforming growth factor-beta / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain ...Transforming growth factor beta-2 proprotein / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Transforming growth factor-beta / Zona pellucida-like 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: To Be Published
Title: Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R)
Authors: Wieteska, L. / Taylor, A.B. / Hinck, A.P.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.6 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

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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

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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

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