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- PDB-6mzn: Zebrafish betaglycan orphan domain structure from tetragonal crys... -

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Basic information

Entry
Database: PDB / ID: 6mzn
TitleZebrafish betaglycan orphan domain structure from tetragonal crystal form
ComponentsTransforming growth factor beta receptor III
KeywordsPROTEIN BINDING / Proteoglycan / cytokine receptor / co-receptor
Function / homology
Function and homology information


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / transforming growth factor beta receptor activity / regulation of transforming growth factor beta receptor signaling pathway / somite development / type II transforming growth factor beta receptor binding ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / transforming growth factor beta receptor activity / regulation of transforming growth factor beta receptor signaling pathway / somite development / type II transforming growth factor beta receptor binding / glycosaminoglycan binding / sprouting angiogenesis / bone mineralization / epithelial to mesenchymal transition / transforming growth factor beta receptor signaling pathway / cell migration / extracellular region / membrane
Similarity search - Function
Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Transforming growth factor beta receptor III / Transforming growth factor, beta receptor III
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHinck, A.P. / Kim, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA172886 United States
CitationJournal: Structure / Year: 2019
Title: Structural Adaptation in Its Orphan Domain Engenders Betaglycan with an Alternate Mode of Growth Factor Binding Relative to Endoglin.
Authors: Kim, S.K. / Whitley, M.J. / Krzysiak, T.C. / Hinck, C.S. / Taylor, A.B. / Zwieb, C. / Byeon, C.H. / Zhou, X. / Mendoza, V. / Lopez-Casillas, F. / Furey, W. / Hinck, A.P.
History
DepositionNov 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 1.4Nov 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 receptor III


Theoretical massNumber of molelcules
Total (without water)37,8191
Polymers37,8191
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.940, 62.940, 114.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Transforming growth factor beta receptor III


Mass: 37819.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: tgfbr3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A0H3UK16, UniProt: E7FDB6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 8% v/v PEG 5K mono methyl ether, 4% w/v PEG 20K, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.38→35.11 Å / Num. obs: 17750 / % possible obs: 99.4 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 7.5 % / Biso Wilson estimate: 70.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.046 / Rrim(I) all: 0.093 / Net I/σ(I): 10.6
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.784 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1873 / CC1/2: 0.52 / Rpim(I) all: 0.786 / Rrim(I) all: 2.104 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLM7.2.2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MZP

6mzp


Resolution: 2.38→27.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1759 9.92 %RANDOM
Rwork0.198 ---
obs0.202 17730 99.4 %-
Displacement parametersBiso mean: 106.14 Å2
Baniso -1Baniso -2Baniso -3
1--7.8089 Å20 Å20 Å2
2---7.8089 Å20 Å2
3---15.6177 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.38→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 0 8 2450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012501HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.273400HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d858SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes354HARMONIC5
X-RAY DIFFRACTIONt_it2501HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion21.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2551SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.254 274 9.52 %
Rwork0.235 2603 -
all0.237 2877 -
obs--99.76 %
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)
13.3428-3.91680.38320.8204-0.168111.0329-0.1087-0.6836-0.5285-0.280.17820.1879-0.4439-0.6717-0.0695-0.18060.01280.02790.00150.0492-0.2865-7.1117-3.07238.0357
24.58721.50751.206911.7822.54247.084-0.74440.2982-0.0444-0.61751.0854-2.0122-0.43671.4651-0.34090.0253-0.19180.1284-0.18-0.20710.009510.91923.788621.1395
34.12930.5156-2.39146.4771-3.7517.8701-0.0037-0.3881-0.7306-0.1202-0.10590.1404-0.135-0.74770.1096-0.2205-0.02220.0164-0.06650.0014-0.1413-6.0693-5.427336.2879
44.0506-2.2734-0.18596.51791.587.74080.136-0.1637-0.6699-1.11830.21160.58980.1469-1.0179-0.3476-0.0605-0.1812-0.0993-0.23930.0088-0.2628-7.7664-9.355626.0115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{A|30 - 48}30 - 48
2X-RAY DIFFRACTION2{A|49 - 215}49 - 215
3X-RAY DIFFRACTION3{A|216 - 232}216 - 232
4X-RAY DIFFRACTION4{A|233 - 359}233 - 359

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