[English] 日本語
Yorodumi
- PDB-4cem: Crystal structure of the first MIF4G domain of human nonsense med... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cem
TitleCrystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2
ComponentsREGULATOR OF NONSENSE TRANSCRIPTS 2
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / liver development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / perinuclear region of cytoplasm ...exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / animal organ regeneration / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / liver development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / perinuclear region of cytoplasm / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsClerici, M. / Deniaud, A. / Boehm, V. / Gehring, N.H. / Schaffitzel, C. / Cusack, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and Functional Analysis of the Three Mif4G Domains of Nonsense-Mediated Decay Factor Upf2.
Authors: Clerici, M. / Deniaud, A. / Boehm, V. / Gehring, N.H. / Schaffitzel, C. / Cusack, S.
History
DepositionNov 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REGULATOR OF NONSENSE TRANSCRIPTS 2
B: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)85,9322
Polymers85,9322
Non-polymers00
Water97354
1
A: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)42,9661
Polymers42,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: REGULATOR OF NONSENSE TRANSCRIPTS 2


Theoretical massNumber of molelcules
Total (without water)42,9661
Polymers42,9661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.080, 101.080, 158.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein REGULATOR OF NONSENSE TRANSCRIPTS 2 / NONSENSE MRNA REDUCING FACTOR 2 / UP-FRAMESHIFT SUPPRESSOR 2 HOMOLOG / HUPF2 / UPF2


Mass: 42965.867 Da / Num. of mol.: 2 / Fragment: MIF4G1, RESIDUES 121-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9HAU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL GAMG LEFT AFTER HIS-TAG CLEAVAGE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 9
Details: 100 MM BICINE PH 9, 100 MM NACL, 11% PEG 6000 AND AT A PROTEIN CONCENTRATION OF 16 MG/ML

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28216 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 2.86 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
SHELXDSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→87.54 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.404 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25087 1428 5.1 %RANDOM
Rwork0.20532 ---
obs0.20761 26788 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→87.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 0 54 5115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195159
X-RAY DIFFRACTIONr_bond_other_d0.0010.023662
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9596938
X-RAY DIFFRACTIONr_angle_other_deg0.81838927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33624.382267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82915984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3391538
X-RAY DIFFRACTIONr_chiral_restr0.060.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021023
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 97 -
Rwork0.327 1942 -
obs--100 %

+
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