[English] 日本語
Yorodumi
- PDB-8rdd: Crystal structure of Saccharomyces cerevisiae Nmd4 protein involv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rdd
TitleCrystal structure of Saccharomyces cerevisiae Nmd4 protein involved in nonsense mediated mRNA decay
ComponentsNonsense-mediated decay protein 4
KeywordsRNA BINDING PROTEIN / Nonsense-mediated mRNA decay / PIN domain
Function / homologyLarge family of predicted nucleotide-binding domains / PIN domain / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nucleus / cytoplasm / ACETIC ACID / Nonsense-mediated decay protein 4
Function and homology information
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsBarbarin-Bocahu, I. / Graille, M.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0003-04 France
Centre National de la Recherche Scientifique (CNRS) France
Ecole polytechnique France
CitationJournal: Plos Biol. / Year: 2024
Title: Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans.
Authors: Barbarin-Bocahu, I. / Ulryck, N. / Rigobert, A. / Ruiz Gutierrez, N. / Decourty, L. / Raji, M. / Garkhal, B. / Le Hir, H. / Saveanu, C. / Graille, M.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nonsense-mediated decay protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8394
Polymers19,6271
Non-polymers2123
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-1 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.371, 80.371, 94.134
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Nonsense-mediated decay protein 4


Mass: 19626.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: NMD4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q12129
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Na citrate, 0.1 M Na cacodylate pH 6.5, 0.2 M lithium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40.2 Å / Num. obs: 31899 / % possible obs: 95.7 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.0015 / Net I/σ(I): 25.7
Reflection shellResolution: 1.8→1.853 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1598 / CC1/2: 0.608 / Rpim(I) all: 0.58

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→40.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1580 -RANDOM
Rwork0.1811 ---
obs0.1816 31899 95.7 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.3052 Å20 Å20 Å2
2--0.3052 Å20 Å2
3----0.6104 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.796→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 14 208 1556
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091404HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.861897HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d509SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes242HARMONIC5
X-RAY DIFFRACTIONt_it1404HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion186SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1357SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.63
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2787 27 -
Rwork0.2918 --
obs0.2912 638 42.38 %
Refinement TLS params.Origin x: -29.5393 Å / Origin y: 24.8888 Å / Origin z: -29.0679 Å
111213212223313233
T-0.0018 Å20.0067 Å20.0015 Å2--0.0476 Å2-0.0004 Å2---0.0381 Å2
L1.3342 °2-0.1481 °2-0.2783 °2-0.8424 °20.3396 °2--1.3547 °2
S0.0436 Å °0.1049 Å °0.0369 Å °0.1049 Å °0.0042 Å °-0.0507 Å °0.0369 Å °-0.0507 Å °-0.0478 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 164
2X-RAY DIFFRACTION1{ B|* }B201 - 206

+
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