[English] 日本語
Yorodumi
- PDB-4wpm: Structure of the Chaetomium thermophilum Mex67:Mtr2 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wpm
TitleStructure of the Chaetomium thermophilum Mex67:Mtr2 Complex
ComponentsmRNA export protein
KeywordsTRANSPORT PROTEIN / mRNA nuclear export
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / RNA binding / nucleus
Similarity search - Function
Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / UBA-like superfamily ...Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Putative mRNA export protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsAibara, S. / Valkov, E. / Stewart, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum.
Authors: Aibara, S. / Valkov, E. / Lamers, M.H. / Dimitrova, L. / Hurt, E. / Stewart, M.
History
DepositionOct 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA export protein
B: mRNA export protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1795
Polymers26,8902
Non-polymers2883
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-28 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.731, 29.796, 52.453
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein mRNA export protein


Mass: 13445.239 Da / Num. of mol.: 2 / Fragment: RRM domain, UNP residues 93-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0059630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SET4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: see publication for details

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.4→40.7 Å / Num. obs: 7066 / % possible obs: 99.6 % / Redundancy: 4 % / Net I/σ(I): 5.7

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.4→40.679 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 323 4.58 %
Rwork0.2286 --
obs0.2294 7056 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→40.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 15 53 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021351
X-RAY DIFFRACTIONf_angle_d0.6771820
X-RAY DIFFRACTIONf_dihedral_angle_d13.044512
X-RAY DIFFRACTIONf_chiral_restr0.029208
X-RAY DIFFRACTIONf_plane_restr0.002229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-3.02370.28471590.28053320X-RAY DIFFRACTION99
3.0237-40.68460.2291640.20343413X-RAY DIFFRACTION99
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)
10.03330.0395-0.03120.0441-0.03640.02770.0286-0.146-0.09110.0486-0.0705-0.0056-0.1341-0.0206-0.00380.15810.00740.00170.13690.04220.179625.8673-2.037316.2746
20.00920.0120.01490.05380.01530.02410.0035-0.0201-0.0094-0.01410.0218-0.07680.01650.01870.01590.10960.0238-0.0270.0695-0.0480.112635.1802-5.35619.263
30.1699-0.0297-0.0760.00540.01180.03520.0974-0.08310.0114-0.183-0.1021-0.11480.01490.05850.04240.12330.02190.07770.11210.03060.08830.94644.16679.8652
40.3822-0.1676-0.22810.19070.15850.17070.08890.10760.0187-0.03920.024-0.09750.0064-0.09760.14910.1677-0.0121-0.04010.0454-0.01290.053324.80242.668710.0348
50.10490.1141-0.12290.2417-0.09540.15370.0932-0.00920.06440.09370.03550.0230.0033-0.00140.06820.08580.0382-0.00430.1892-0.01120.23787.356711.647825.9834
60.0018-0.00390.00310.009-0.0080.00620.01060.04730.0336-0.02-0.01710.0222-0.0113-0.00230.01320.05250.0784-0.07480.1574-0.01370.16365.508316.896918.252
70.0038-0.0044-0.00150.01030.00590.0033-0.0739-0.0322-0.01050.1241-0.030.04740.0597-0.0605-0.00010.4828-0.1318-0.1330.36960.04740.33834.092411.981612.1337
80.0229-0.00640.01960.0704-0.030.0413-0.0977-0.0871-0.0326-0.0594-0.09550.01870.009-0.024-0.04960.1179-0.01880.01380.1192-0.0240.117710.58888.927519.6393
90.0351-0.00570.09190.0894-0.12030.3704-0.0450.0056-0.05020.007-0.0341-0.0103-0.02320.0913-0.01060.115-0.07290.10520.04240.01540.246510.23330.3522.7885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 171 )
9X-RAY DIFFRACTION9chain 'B' and (resid 172 through 181 )

+
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