[English] 日本語
Yorodumi
- PDB-7qg6: Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qg6
TitleCo-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII
Components
  • Regulator of nonsense transcripts 2
  • Regulator of nonsense transcripts 3A
KeywordsRNA BINDING PROTEIN / nonsense mediated mRNA decay neurological development x-linked intellectual disability up-frameshift proteins
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / mRNA transport / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of translation ...positive regulation of mRNA cis splicing, via spliceosome / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / mRNA transport / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of translation / liver development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / spermatogenesis / in utero embryonic development / neuron projection / intracellular membrane-bounded organelle / mRNA binding / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA-binding domain superfamily ...Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Regulator of nonsense transcripts 3A / Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPowers, K.T. / Bufton, J.C. / Szeto, J.A. / Schaffitzel, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210701/Z/18/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
Authors: Bufton, J.C. / Powers, K.T. / Szeto, J.A. / Toelzer, C. / Berger, I. / Schaffitzel, C.
History
DepositionDec 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
A: Regulator of nonsense transcripts 3A
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,97112
Polymers234,4868
Non-polymers4864
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, picomolar affinity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-14 kcal/mol
Surface area18380 Å2
MethodPISA
2
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-16 kcal/mol
Surface area18030 Å2
MethodPISA
3
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-14 kcal/mol
Surface area18030 Å2
MethodPISA
4
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-11 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.677, 108.579, 119.943
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Regulator of nonsense transcripts 3A / Nonsense mRNA reducing factor 3A / Up-frameshift suppressor 3 homolog A / hUpf3


Mass: 20829.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF3A, RENT3A, UPF3 / Plasmid: pPROEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H1J1
#2: Protein
Regulator of nonsense transcripts 2 / Up-frameshift suppressor 2 homolog / hUpf2


Mass: 37791.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF2, KIAA1408, RENT2 / Plasmid: pPROEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HAU5
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.94 Å3/Da / Density % sol: 58.11 % / Description: cubic spinel
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Temp details: 20C

-
Data collection

DiffractionMean temperature: 277 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationMonochromator: cPGM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.95→65.25 Å / Num. obs: 41731 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 66.66 Å2 / Rpim(I) all: 0.087 / Net I/σ(I): 7.2
Reflection shellResolution: 2.95→3.02 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2660 / Rpim(I) all: 0.5 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uw4

1uw4


Resolution: 2.95→65.25 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 2080 4.99 %
Rwork0.2069 39630 -
obs0.2096 41710 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.32 Å2 / Biso mean: 66.928 Å2 / Biso min: 23.2 Å2
Refinement stepCycle: final / Resolution: 2.95→65.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11685 0 31 19 11735
Biso mean--69.17 50.83 -
Num. residues----1458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.020.38781330.320926602793100
3.02-3.090.3751200.288726762796100
3.09-3.180.34931560.27292602275899
3.18-3.270.33121810.26132577275899
3.27-3.380.32461320.24472658279099
3.38-3.50.3121220.241926472769100
3.5-3.640.30271320.22962637276999
3.64-3.80.27661470.22952619276699
3.8-40.24541270.1992673280099
4-4.250.26311350.18552612274799
4.25-4.580.20431360.17312661279799
4.58-5.040.21621450.16682604274999
5.04-5.770.25551640.18922645280999
5.77-7.270.26171290.22242655278499
7.28-65.250.20961210.17262704282598

+
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