[English] 日本語
Yorodumi
- PDB-3q0s: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q0s
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO2 in complex with erk2 NRE
Components
  • 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'
  • Pumilio homolog 2
KeywordsRNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex
Function / homology
Function and homology information


positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / positive regulation of RIG-I signaling pathway / regulation of chromosome segregation / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding ...positive regulation of sprouting of injured axon / pumilio-response element binding / regulation of intracellular mRNA localization / regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / positive regulation of RIG-I signaling pathway / regulation of chromosome segregation / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / lncRNA binding / regulation of postsynapse assembly / hair follicle development / chromosome organization / adipose tissue development / regulation of mRNA stability / stress granule assembly / respiratory electron transport chain / mRNA 3'-UTR binding / skeletal system development / mitochondrion organization / cytoplasmic stress granule / regulation of translation / Neddylation / nuclear membrane / postsynapse / neuronal cell body / perinuclear region of cytoplasm / glutamatergic synapse / RNA binding / cytosol / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / Pumilio homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLu, G. / Hall, T.M.T.
CitationJournal: Structure / Year: 2011
Title: Alternate modes of cognate RNA recognition by human PUMILIO proteins.
Authors: Lu, G. / Hall, T.M.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pumilio homolog 2
B: 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)43,0122
Polymers43,0122
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.404, 45.364, 97.800
Angle α, β, γ (deg.)90.00, 125.26, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pumilio homolog 2 / Pumilio-2


Mass: 40524.719 Da / Num. of mol.: 1 / Fragment: UNP residues 706-1056
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUM2, KIAA0235, PUMH2 / Plasmid: pDEST527 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8TB72
#2: RNA chain 5'-R(UP*GP*UP*AP*CP*AP*UP*C)-3'


Mass: 2487.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA sequence occurs naturally in humans.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 17-20% (w/v) PEG 3000, 100 mM Na3Citrate pH 5.0-6.0 , VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 14, 2008
RadiationMonochromator: varimax hf / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24 Å / Num. all: 28271 / Num. obs: 26134 / % possible obs: 92.44 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 93

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.4_6)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24 Å / SU ML: 1.18 / σ(F): 0.03 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1279 4.89 %Random
Rwork0.2066 ---
all0.2087 26134 --
obs0.2087 26134 92.44 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.201 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4583 Å20 Å2-2.353 Å2
2--17.6275 Å2-0 Å2
3----16.1692 Å2
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 164 0 136 3083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063019
X-RAY DIFFRACTIONf_angle_d0.8644103
X-RAY DIFFRACTIONf_dihedral_angle_d18.9931171
X-RAY DIFFRACTIONf_chiral_restr0.055463
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.07990.33441220.24662410X-RAY DIFFRACTION81
2.0799-2.17450.26911430.21592733X-RAY DIFFRACTION93
2.1745-2.28910.25591360.19012728X-RAY DIFFRACTION92
2.2891-2.43240.29931340.19312707X-RAY DIFFRACTION91
2.4324-2.61990.27321290.20882688X-RAY DIFFRACTION90
2.6199-2.88320.26331510.20782710X-RAY DIFFRACTION92
2.8832-3.29950.29011440.22222840X-RAY DIFFRACTION95
3.2995-4.15350.20251460.17253014X-RAY DIFFRACTION100
4.1535-24.02710.21931740.19823025X-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)
10.3840.31040.0660.29450.04860.77810.04240.78880.2871-0.1999-0.17770.0733-0.39530.3645-0.00040.24840.0708-0.00710.57780.07160.30177.216517.87238.6764
21.04620.9638-0.01540.6817-0.12560.81630.05220.6935-0.01080.0230.17890.00710.18030.19220.00010.20960.0527-0.01980.4833-0.04420.2475-0.24178.117110.7421
30.41820.3964-0.63491.0371-1.21571.2736-0.08520.49080.09650.2710.15940.0230.37570.1137-0.00010.29140.1009-0.02310.2567-0.03240.2332-2.2871-1.788616.5247
40.80260.6495-1.00160.5872-0.67011.17510.03380.35630.1002-0.3598-0.03790.16050.520.17490.00010.41080.0571-0.04860.2167-0.01830.2627-5.3735-9.111624.2592
50.50660.0919-0.68780.28220.12720.99360.30440.2222-0.0712-0.1122-0.1860.01880.33810.028400.35120.0475-0.05490.1358-0.02340.2922-8.8725-12.034434.5164
60.5474-0.0685-0.39540.11760.40891.06890.29790.0374-0.14660.1965-0.09690.08440.5944-0.37630.00010.325-0.0477-0.08140.19450.02860.2769-14.4316-11.699743.5233
70.0373-0.0093-0.12180.55530.79960.8940.3024-0.27750.01520.0531-0.08460.09430.1804-0.66060.00010.197-0.0274-0.01810.35740.04030.2509-19.8414-6.79452.5038
80.0655-0.23780.25121.3939-0.20360.72220.5274-0.19740.37940.0918-0.15740.4763-0.2647-1.20250.00020.19190.090.03770.6823-0.03830.4038-25.1102-0.303660.3027
90.9231-0.2929-0.05950.97230.7180.6180.6415-1.26480.07890.4643-0.34920.1619-1.0668-1.67880.02020.43070.30810.10721.0601-0.23380.5242-27.15668.269367.2644
100.3249-0.04420.18750.0424-0.03370.54130.7707-1.18870.45480.130.1386-0.2664-0.8891-2.550.00961.23150.35950.09791.1649-0.19611.0726-24.284718.554366.0835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 706:729)
2X-RAY DIFFRACTION2(chain A and resid 730:766)
3X-RAY DIFFRACTION3(chain A and resid 767:802)
4X-RAY DIFFRACTION4(chain A and resid 803:840)
5X-RAY DIFFRACTION5(chain A and resid 841:876)
6X-RAY DIFFRACTION6(chain A and resid 877:912)
7X-RAY DIFFRACTION7(chain A and resid 913:948)
8X-RAY DIFFRACTION8(chain A and resid 949:984)
9X-RAY DIFFRACTION9(chain A and resid 985:1027)
10X-RAY DIFFRACTION10(chain A and resid 1028:1049)

+
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