[English] 日本語
Yorodumi
- PDB-3bx3: Puf4 T650C/C724R Mutant bound to Cox17 RNA 3' UTR recognition sequence -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bx3
TitlePuf4 T650C/C724R Mutant bound to Cox17 RNA 3' UTR recognition sequence
Components
  • COX17 RNA target sequence
  • Protein PUF4
KeywordsTRANSCRIPTION / RNA BINDING PROTEIN/RNA / Puf4 / Pumilio / RNA Binding / HO endonuclease / Puf4 T650C C724R mutant / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / protein localization / negative regulation of translation / mRNA binding / 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 homology domain family member 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiller, M.T. / Higgin, J.J. / Hall, T.M.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p
Authors: Miller, M.T. / Higgin, J.J. / Hall, T.M.T.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: COX17 RNA target sequence
D: COX17 RNA target sequence
A: Protein PUF4
B: Protein PUF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,93713
Polymers81,0724
Non-polymers8659
Water0
1
C: COX17 RNA target sequence
A: Protein PUF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0177
Polymers40,5362
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: COX17 RNA target sequence
B: Protein PUF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9206
Polymers40,5362
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.065, 137.116, 160.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain COX17 RNA target sequence


Mass: 2512.529 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Protein PUF4


Mass: 38023.664 Da / Num. of mol.: 2 / Fragment: Single Stranded RNA Binding Domin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25339
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2 M Ammonium Sulfate, 100 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2Tris11
3(NH4)2SO412
4Tris12

-
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 7, 2007
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→24.4 Å / Num. all: 30974 / Num. obs: 29415 / % possible obs: 94.7 % / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.1 Å / % possible all: 94.7

-
Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.4 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.35 1500 RANDOM
Rwork0.29 --
all0.291 30003 -
obs-29415 -
Refinement stepCycle: LAST / Resolution: 3→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 332 45 0 5349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.383
LS refinement shellResolution: 3→3.01 Å
RfactorNum. reflection% reflection
Rwork0.35 --
obs-263 50 %

+
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