[English] 日本語
Yorodumi
- PDB-9ftw: Crystal structure of calcium-activated EndoU -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ftw
TitleCrystal structure of calcium-activated EndoU
ComponentsUridylate-specific endoribonuclease
KeywordsRNA BINDING PROTEIN / calcium
Function / homology
Function and homology information


post-transcriptional gene silencing / scavenger receptor activity / polysaccharide binding / negative regulation of lipid catabolic process / RNA endonuclease activity / serine-type peptidase activity / female pregnancy / growth factor activity / Lyases; Phosphorus-oxygen lyases / manganese ion binding ...post-transcriptional gene silencing / scavenger receptor activity / polysaccharide binding / negative regulation of lipid catabolic process / RNA endonuclease activity / serine-type peptidase activity / female pregnancy / growth factor activity / Lyases; Phosphorus-oxygen lyases / manganese ion binding / lyase activity / immune response / proteolysis / RNA binding / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Eukaryotic uridylate-specific endoribonuclease (EndoU) domain profile. / EndoU ribonuclease, C-terminal / Poly(U)-specific endoribonuclease / Endoribonuclease XendoU / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. ...Eukaryotic uridylate-specific endoribonuclease (EndoU) domain profile. / EndoU ribonuclease, C-terminal / Poly(U)-specific endoribonuclease / Endoribonuclease XendoU / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Endoribonuclease EndoU-like
Similarity search - Domain/homology
ACETATE ION / Uridylate-specific endoribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFribourg, S. / Campagne, S.
Funding support France, 1items
OrganizationGrant numberCountry
Institut National de la Sante et de la Recherche Medicale (INSERM) France
Citation
Journal: Res Sq / Year: 2024
Title: Molecular Basis for the Calcium-Dependent Activation of the Ribonuclease EndoU.
Authors: Malard, F. / Dias, K. / Baudy, M. / Thore, S. / Vialet, B. / Barthelemy, P. / Fribourg, S. / Karginov, F.V. / Campagne, S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,37814
Polymers93,8562
Non-polymers52212
Water7,512417
1
A: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2508
Polymers46,9281
Non-polymers3227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1296
Polymers46,9281
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.723, 49.742, 60.946
Angle α, β, γ (deg.)88.62, 87.49, 70.35
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Uridylate-specific endoribonuclease / Placental protein 11 / PP11 / Protein endoU


Mass: 46928.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOU / Production host: Escherichia coli (E. coli)
References: UniProt: P21128, Lyases; Phosphorus-oxygen lyases
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Na Acetate 0.1 M HEPES pH 7.5 22 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→47 Å / Num. obs: 59530 / % possible obs: 93.9 % / Redundancy: 1.92 % / Biso Wilson estimate: 22.39 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.81
Reflection shellResolution: 1.65→1.67 Å / Num. unique obs: 8577 / CC1/2: 0.88 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→23.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.105
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 2835 4.77 %RANDOM
Rwork0.1881 ---
obs0.1895 59460 93.8 %-
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.6174 Å2-0.6386 Å2-2.9145 Å2
2---1.3215 Å2-2.8303 Å2
3---2.9389 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 18 417 4943
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018927HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9615992HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2615SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1450HARMONIC5
X-RAY DIFFRACTIONt_it4657HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion15.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
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_contact8164SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.67 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.258 -5.04 %
Rwork0.2394 1130 -
all0.2404 1190 -
obs--67.93 %
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)
11.2762-0.1104-0.30290.8899-0.1440.7890.20370.20350.1673-0.0802-0.1487-0.0859-0.0269-0.0525-0.055-0.00650.04440.0268-0.00450.0344-0.047-18.7415-4.2152-9.4314
21.1668-0.35530.02190.8175-0.07330.63-0.1254-0.1442-0.09190.09390.14370.112-0.00650.0266-0.0183-0.02750.01050.009-0.02460.0083-0.0586-3.4815-26.995-40.3822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ A|* }

+
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://pdbjlc1.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