[English] 日本語
Yorodumi
- PDB-8r2c: Crystal structure of the Vint domain from Tetrahymena thermophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r2c
TitleCrystal structure of the Vint domain from Tetrahymena thermophila
Componentsvon willebrand factor type A (VWA) domain was originally protein
KeywordsUNKNOWN FUNCTION / hedgehog / Vint / intein / HINT / von Willebrand factor type A domain
Function / homology
Function and homology information


intein-mediated protein splicing
Similarity search - Function
VWA-Hint protein, Vwaint domain / VWA / Hh protein intein-like / : / Vint domain / Hint-domain / von Willebrand factor type A domain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain superfamily / von Willebrand factor (vWF) type A domain ...VWA-Hint protein, Vwaint domain / VWA / Hh protein intein-like / : / Vint domain / Hint-domain / von Willebrand factor type A domain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / von willebrand factor type A (VWA) domain was originally protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIwai, H. / Beyer, H.M. / Johannson, J.E. / Li, M. / Wlodawer, A.
Funding support Finland, Denmark, United States, 6items
OrganizationGrant numberCountry
Academy of Finland131413 Finland
Academy of Finland137995 Finland
Academy of Finland277335 Finland
Novo Nordisk FoundationNNF17OC0025402 Denmark
Novo Nordisk FoundationNNF17OC0027550 Denmark
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: Febs Lett. / Year: 2024
Title: The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold.
Authors: Iwai, H. / Beyer, H.M. / Johansson, J.E.M. / Li, M. / Wlodawer, A.
History
DepositionNov 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: von willebrand factor type A (VWA) domain was originally protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9489
Polymers19,1491
Non-polymers7998
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-71 kcal/mol
Surface area8370 Å2
Unit cell
Length a, b, c (Å)35.890, 46.360, 115.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein von willebrand factor type A (VWA) domain was originally protein


Mass: 19149.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote)
Gene: TTHERM_00471620 / Plasmid: pBHRSF123 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: I7M030
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100 nL concentrated protein (14.6 mg/mL) with 100 nL mother liquid (2% PEG 400, 2.4 M ammonium sulfate, 0.1 M HEPES)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 18445 / % possible obs: 97.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.63 Å2 / Rmerge(I) obs: 0.0157 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.1109 / Num. unique obs: 1737

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43 Å / SU ML: 0.2045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 568 3.09 %
Rwork0.1886 17822 -
obs0.1898 18390 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 46 92 1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211406
X-RAY DIFFRACTIONf_angle_d1.29221888
X-RAY DIFFRACTIONf_chiral_restr0.0653203
X-RAY DIFFRACTIONf_plane_restr0.0077234
X-RAY DIFFRACTIONf_dihedral_angle_d11.5738192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.29071280.25964322X-RAY DIFFRACTION98.21
1.98-2.270.25931160.19954422X-RAY DIFFRACTION99.87
2.27-2.860.26631640.1974428X-RAY DIFFRACTION99.7
2.86-430.1871600.1674650X-RAY DIFFRACTION99.83

+
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