[English] 日本語
Yorodumi
- PDB-1koh: THE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BIND... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1koh
TitleTHE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BINDING DOMAIN FOUND IN THE HUMAN TAP NUCLEAR MRNA EXPORT FACTOR
ComponentsTIP ASSOCIATING PROTEIN
KeywordsRNA BINDING PROTEIN / mRNA export factor / Constitutive transport element (CTE) Ribonucleoprotein (RNP) and Leucine Rich Repeat (LRR) domains
Function / homology
Function and homology information


nuclear RNA export factor complex / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule ...nuclear RNA export factor complex / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule / protein transport / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / 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. / Nuclear transport factor 2 domain ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / 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. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / UBA-like superfamily / RRM (RNA recognition motif) domain / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear RNA export factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsHo, D.N. / Coburn, G.A. / Kang, Y. / Cullen, B.R. / Georgiadis, M.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor.
Authors: Ho, D.N. / Coburn, G.A. / Kang, Y. / Cullen, B.R. / Georgiadis, M.M.
#1: Journal: Genes Dev. / Year: 2001
Title: Using viral species specificity to define a critical protein/RNA interaction surface
Authors: Coburn, G.A. / Wiegand, H.L. / Kang, Y. / Ho, D.N. / Georgiadis, M.M. / Cullen, B.R.
#2: Journal: Embo J. / Year: 2000
Title: THE STRUCTURE OF THE MRNA EXPORT FACTOR TAP REVEALS A CIS ARRANGEMENT OF A NON-CANONICAL RNP DOMAIN AND AN LRR DOMAIN
Authors: Liker, E. / Fernandez, E. / Izaurralde, E. / Conti, E.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: 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
A: TIP ASSOCIATING PROTEIN
B: TIP ASSOCIATING PROTEIN
C: TIP ASSOCIATING PROTEIN
D: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)125,9314
Polymers125,9314
Non-polymers00
Water0
1
A: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,4831
Polymers31,4831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,4831
Polymers31,4831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,4831
Polymers31,4831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,4831
Polymers31,4831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.779, 136.779, 202.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
TIP ASSOCIATING PROTEIN / TAP


Mass: 31482.848 Da / Num. of mol.: 4 / Fragment: RESIDUES 96-372 / Mutation: C143S,C252S,C328S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBU9

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium potassium tartrate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
21.1 Mpotassium/sodium tartrate1reservoir
30.05 Msodium citrate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 6, 2000 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 21079 / Num. obs: 18686 / % possible obs: 94.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.1 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.6
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 1 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1900 / Rsym value: 0.578 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.7 %
Reflection shell
*PLUS
% possible obs: 99.6 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FT8

1ft8


Resolution: 3.8→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.355 481 -RANDOM
Rwork0.275 ---
all-17348 --
obs-16469 94.9 %-
Refinement stepCycle: LAST / Resolution: 3.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 0 6854
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

+
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