[English] 日本語
Yorodumi
- PDB-6mzp: Zebrafish betaglycan orphan domain structure from orthorhombic cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mzp
TitleZebrafish betaglycan orphan domain structure from orthorhombic 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 / MIRAS / Resolution: 2.1 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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming growth factor beta receptor III
B: Transforming growth factor beta receptor III


Theoretical massNumber of molelcules
Total (without water)75,6382
Polymers75,6382
Non-polymers00
Water1,42379
1
A: Transforming growth factor beta receptor III


Theoretical massNumber of molelcules
Total (without water)37,8191
Polymers37,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming growth factor beta receptor III


Theoretical massNumber of molelcules
Total (without water)37,8191
Polymers37,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.520, 107.270, 113.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Transforming growth factor beta receptor III


Mass: 37819.184 Da / Num. of mol.: 2
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.: 79 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 9.2% v/v PEG 5K mono methyl ether, 4.6% w/v PEG 20K, 0.1M MES pH 6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9692 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9692 Å / Relative weight: 1
ReflectionResolution: 2.1→40.98 Å / Num. obs: 45850 / % possible obs: 99.9 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 11.6 % / Biso Wilson estimate: 46.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.053 / Rrim(I) all: 0.137 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 11.2 % / Rmerge(I) obs: 2.493 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3715 / CC1/2: 0.565 / Rpim(I) all: 1.069 / Rrim(I) all: 2.719 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLM7.2.2data reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→40.98 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2267 4.94 %RANDOM
Rwork0.232 ---
obs0.233 45850 99.9 %-
Displacement parametersBiso mean: 73.72 Å2
Baniso -1Baniso -2Baniso -3
1-5.3303 Å20 Å20 Å2
2---10.7446 Å20 Å2
3---5.4143 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.1→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 0 0 79 4882
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014912HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.176670HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2265SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4912HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion3.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion647SEMIHARMONIC5
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_contact5168SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 157 4.73 %
Rwork0.244 3160 -
all0.244 3317 -
obs--99.38 %
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)
12.0563.2380.91970.97113.78297.0869-0.0159-0.4633-0.18290.351-0.0925-0.10810.28550.06180.1084-0.0548-0.1782-0.03690.2170.1287-0.133818.6638-6.851117.39
24.0308-0.9093-1.46623.53280.64865.76960.30170.02440.31070.1375-0.16930.0933-0.4634-0.2126-0.1324-0.15090.07540.09080.0018-0.0907-0.0678-9.11610.7938-1.3055
39.0217-0.97416.73424.0408-0.335810.22970.0549-0.3103-0.0932-0.1595-0.0052-0.18030.02290.3307-0.0497-0.1108-0.1792-0.02040.06580.1166-0.263119.729-5.779215.4685
45.7010.6305-1.49992.9909-0.53926.29840.28930.0801-0.5139-0.3651-0.0812-0.32250.80280.1886-0.2082-0.15910.0091-0.0403-0.1140.0335-0.248625.0342-8.3445.3756
51.4607-2.1022.04722.7546-0.93829.10440.094-0.5947-0.50620.55190.2056-0.16430.78210.0489-0.2996-0.05960.1019-0.0103-0.029-0.0479-0.22548.0273-4.4936-11.3222
64.37281.21341.153414.11389.463611.7724-0.20840.4803-0.6539-1.281.7364-2.0293-1.24791.9012-1.528-0.2805-0.33050.17920.0581-0.4103-0.079128.773120.5266-25.9033
72.8530.67431.03464.9023-4.96879.02470.1039-0.3353-0.46610.38590.1658-0.29180.5505-0.0042-0.2698-0.18170.066-0.0158-0.2086-0.0953-0.27589.4965-5.4944-12.4981
83.85990.40662.36564.83752.01814.89540.59960.3653-0.673-0.08240.4361-0.04431.84030.8332-1.0357-0.11560.2041-0.1679-0.178-0.1821-0.26277.6484-10.1018-23.7636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|30 - A|48 }A30 - 48
2X-RAY DIFFRACTION2{ A|49 - A|215 }A49 - 215
3X-RAY DIFFRACTION3{ A|216 - A|232 }A216 - 232
4X-RAY DIFFRACTION4{ A|233 - A|359 }A233 - 359
5X-RAY DIFFRACTION5{ B|30 - B|48 }B30 - 48
6X-RAY DIFFRACTION6{ B|49 - B|215 }B49 - 215
7X-RAY DIFFRACTION7{ B|216 - B|231 }B216 - 231
8X-RAY DIFFRACTION8{ B|234 - B|357 }B234 - 357

+
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