[English] 日本語
Yorodumi
- PDB-1po6: Crystal Structure of UP1 Complexed With d(TAGG(6MI)TTAGGG): A Hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1po6
TitleCrystal Structure of UP1 Complexed With d(TAGG(6MI)TTAGGG): A Human Telomeric Repeat Containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6MI)
Components
  • 5'-D(*T*AP*GP*GP*(6MI)P*TP*TP*AP*GP*GP*G)-3'
  • Heterogeneous nuclear ribonucleoprotein A1
KeywordsRNA Binding Protein/DNA / protein-DNA complex / UP1 / human telomeric repeat / hTR / TR2-6F / RRM / RNA Recognition Motif / 6MI / 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine / hnRNP A1 / RNA Binding Protein-DNA COMPLEX
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / localization / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMyers, J.C. / Moore, S.A. / Shamoo, Y.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures
Authors: Myers, J.C. / Moore, S.A. / Shamoo, Y.
History
DepositionJun 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*T*AP*GP*GP*(6MI)P*TP*TP*AP*GP*GP*G)-3'
A: Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)24,3932
Polymers24,3932
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.807, 51.807, 172.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: DNA chain 5'-D(*T*AP*GP*GP*(6MI)P*TP*TP*AP*GP*GP*G)-3'


Mass: 3511.306 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: OLIGONUCLEOTIDE D(TAGG(6MI)TTAGGG) BASED ON HUMAN TELOMERIC REPEAT D(TTAGGG)N
#2: Protein Heterogeneous nuclear ribonucleoprotein A1 / Helix-destabilizing protein / Single-strand binding protein / hnRNP core protein A1


Mass: 20881.520 Da / Num. of mol.: 1 / Fragment: residues 8-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRPA1 / Plasmid: pYS45 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P09651
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium phosphate11
2glycerol11
3Tris11
4sodium chloride11
5MES11
6EDTAEthylenediaminetetraacetic acid11
7beta-mercaptoethanol2-Mercaptoethanol11
8H2O11
9ammonium phosphate12
10sodium chloride12
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH8.5
215 %(v/v)1reservoir
31.8-2.2 Mdibasic ammonium phosphate1reservoir
41
51
61
71
81
91
101

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2002 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→19.89 Å / Num. all: 15376 / Num. obs: 13930 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.4 / Num. unique all: 722 / Rsym value: 0.501 / % possible all: 96.3
Reflection
*PLUS
% possible obs: 96 %

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UP1

2up1


Resolution: 2.1→19.89 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 694 -Random
Rwork0.234 ---
obs0.234 13930 96.2 %-
all-14484 --
Displacement parametersBiso mean: 24.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.09 Å20 Å20 Å2
2--5.09 Å20 Å2
3----10.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 234 0 155 1855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.5
X-RAY DIFFRACTIONx_torsion_impr_deg3.56
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection% reflection
Rfree0.306 93 -
Rwork0.299 --
obs--89.9 %
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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