[English] 日本語
Yorodumi
- PDB-1uw4: The structural basis of the interaction between nonsense mediated... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uw4
TitleThe structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3
Components
  • REGULATOR OF NONSENSE TRANSCRIPTS 2
  • UPF3X
KeywordsRNA BINDING PROTEIN / NONSENSE MEDIATED MRNA DECAY PROTEIN / RNA-BINDING PROTEIN / NMD / RNP DOMAIN / MIF4G DOMAIN
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / mRNA transport / mRNA export from nucleus ...positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / 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 neuron differentiation / mRNA Splicing - Major Pathway / positive regulation of translation / liver development / brain development / centriolar satellite / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / neuron projection development / neuronal cell body / mRNA binding / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
UPF3B, RNA recognition motif-like domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...UPF3B, RNA recognition motif-like domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Regulator of nonsense transcripts 3B / Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKadlec, J. / Izaurralde, E. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Structural Basis for the Interaction between Nonsense-Mediated Mrna Decay Factors Upf2 and Upf3
Authors: Kadlec, J. / Izaurralde, E. / Cusack, S.
History
DepositionJan 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF3X
B: REGULATOR OF NONSENSE TRANSCRIPTS 2
C: UPF3X
D: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5176
Polymers80,3614
Non-polymers1562
Water5,657314
1
A: UPF3X
B: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2583
Polymers40,1802
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-10.4 kcal/mol
Surface area21560 Å2
MethodPQS
2
C: UPF3X
D: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2583
Polymers40,1802
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9.1 kcal/mol
Surface area21670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.306, 100.178, 153.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2067-

HOH

21D-2079-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9945, -0.104, 0.0131), (-0.1041, 0.9945, -0.0075), (-0.0122, -0.0089, -0.9999)141.4101, 8.2411, 229.6434
2given(-0.9938, -0.1085, 0.0224), (-0.1087, 0.994, -0.0087), (-0.0213, -0.0111, -0.9997)142.37511, 8.8348, 228.99249

-
Components

#1: Protein UPF3X / RNA PROCESSING PROTEIN / UPF3B


Mass: 10902.323 Da / Num. of mol.: 2 / Fragment: RRM DOMAIN, RESIDUES 50-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA-CELL / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BZI7
#2: Protein REGULATOR OF NONSENSE TRANSCRIPTS 2 / UPF2


Mass: 29278.039 Da / Num. of mol.: 2 / Fragment: MIF4G DOMAIN, RESIDUES 768-1015
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA-CELL / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HAU5
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.2 %
Crystal growpH: 6.5
Details: 100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris1droppH7.0
3100 mM1dropNaCl
410 mMbeta-mercaptoethanol1drop
5100 mMammonium acetate1reservoir
615 mMmagnesium acetate1reservoir
750 mMsodium cacodylate1reservoirpH6.5
88 %(v/v)isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9792, 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97921
30.97951
ReflectionResolution: 1.95→33.7 Å / Num. obs: 79316 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.74
Reflection shellResolution: 1.95→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.3 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Redundancy: 4.3 % / Num. measured all: 338871 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.305

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.531 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2379 3 %RANDOM
Rwork0.204 ---
obs0.205 76925 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 2 314 5973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225827
X-RAY DIFFRACTIONr_bond_other_d0.0020.025295
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9587890
X-RAY DIFFRACTIONr_angle_other_deg0.8312327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021246
X-RAY DIFFRACTIONr_nbd_refined0.1970.21130
X-RAY DIFFRACTIONr_nbd_other0.2170.25699
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4881.53413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92725574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57732414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5984.52316
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 167
Rwork0.26 5413
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)
10.77870.1350.13480.62230.13410.895-0.0362-0.09720.08170.15920.0251-0.0063-0.11690.01040.01110.15520.0116-0.02990.0689-0.0230.054273.03221.881138.012
21.0661-0.17860.27440.8998-0.29731.1172-0.01790.11240.1373-0.0925-0.01160.0113-0.1465-0.00790.02960.0171-0.0094-0.01930.00740.01810.046265.48721.31192.247
32.1064-0.3078-0.70522.3592-0.55012.6622-0.04110.09260.0729-0.1530.0223-0.5449-0.22210.4320.01880.1583-0.1105-0.07980.2176-0.05340.260994.05621.739127.631
42.17050.1254-0.63782.6050.37392.22660.0077-0.14890.06350.2404-0.04610.6212-0.1705-0.40520.03840.04280.069-0.00760.15360.01010.248444.38119.135102.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B768 - 1015
2X-RAY DIFFRACTION2D768 - 1015
3X-RAY DIFFRACTION3A50 - 140
4X-RAY DIFFRACTION4C50 - 140
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12

+
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