[English] 日本語
Yorodumi
- PDB-3q0p: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q0p
TitleCrystal structure of the PUMILIO-homology domain from Human PUMILIO1 in complex with hunchback NRE
Components
  • 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
  • Pumilio homolog 1
KeywordsRNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis ...regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis / mRNA destabilization / regulation of mRNA stability / adult locomotory behavior / mRNA 3'-UTR binding / stem cell differentiation / P-body / cytoplasmic stress granule / regulation of translation / spermatogenesis / regulation of cell cycle / axon / RNA binding / nucleoplasm / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pumilio homolog 1
B: Pumilio homolog 1
C: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
D: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8256
Polymers85,7544
Non-polymers712
Water2,486138
1
A: Pumilio homolog 1
C: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9133
Polymers42,8772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-7 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: Pumilio homolog 1
D: 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9133
Polymers42,8772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.326, 37.483, 82.299
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pumilio homolog 1 / HsPUM / Pumilio-1


Mass: 40364.523 Da / Num. of mol.: 2 / Fragment: UNP residues 828-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUM1, KIAA0099, PUMH1 / Plasmid: pTYB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14671
#2: RNA chain 5'-R(UP*GP*UP*AP*UP*AP*UP*A)-3'


Mass: 2512.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This RNA occurs in flies.
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 15-20% (w/v) PEG 3350, 100 mM Li2SO4, and 100 mM Na3Citrate pH 5.5-6.0 , 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: Aug 24, 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: 2.6→23.8 Å / Num. all: 24731 / Num. obs: 22777 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 95.1

-
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: 2.6→23.786 Å / SU ML: 2.04 / σ(F): 0.06 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 1148 5.04 %Random
Rwork0.193 ---
all0.1965 22777 --
obs0.1965 22777 92.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.714 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3698 Å20 Å2-0.3117 Å2
2--3.1271 Å2-0 Å2
3---1.2427 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 332 2 138 5962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055973
X-RAY DIFFRACTIONf_angle_d0.9028138
X-RAY DIFFRACTIONf_dihedral_angle_d19.152293
X-RAY DIFFRACTIONf_chiral_restr0.06918
X-RAY DIFFRACTIONf_plane_restr0.0031004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71760.31231420.21062441X-RAY DIFFRACTION84
2.7176-2.86070.33861250.21822486X-RAY DIFFRACTION86
2.8607-3.03960.29931300.22192534X-RAY DIFFRACTION87
3.0396-3.27370.30841240.21482705X-RAY DIFFRACTION93
3.2737-3.60210.26271440.18612831X-RAY DIFFRACTION96
3.6021-4.1210.25541560.1672827X-RAY DIFFRACTION96
4.121-5.18320.21691430.15822836X-RAY DIFFRACTION96
5.1832-23.78680.23161840.1942969X-RAY DIFFRACTION98

+
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