[English] 日本語
Yorodumi
- PDB-6lur: Human PUF60 UHM domain (thioredoxin fusion) in complex with a sma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lur
TitleHuman PUF60 UHM domain (thioredoxin fusion) in complex with a small molecule binder
ComponentsThioredoxin 1,Poly(U)-binding-splicing factor PUF60
KeywordsSPLICING / splicing factor
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / DNA polymerase processivity factor activity / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell redox homeostasis / cell junction / cadherin binding / ribonucleoprotein complex ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / DNA polymerase processivity factor activity / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell redox homeostasis / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / : / RNA recognition motif domain, eukaryote / RNA recognition motif / Thioredoxin / Thioredoxin / Thioredoxin, conserved site ...Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / : / RNA recognition motif domain, eukaryote / RNA recognition motif / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / RRM (RNA recognition motif) domain / Thioredoxin domain profile. / Thioredoxin domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EVU / Thioredoxin 1 / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTakahashi, M. / Hanzawa, H.
CitationJournal: J.Biomol.Nmr / Year: 2020
Title: Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery.
Authors: Hanzawa, H. / Shimada, T. / Takahashi, M. / Takahashi, H.
History
DepositionJan 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
B: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
C: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
D: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
E: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
F: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
G: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
H: Thioredoxin 1,Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,62616
Polymers197,3758
Non-polymers2,2518
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24190 Å2
ΔGint-79 kcal/mol
Surface area72670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.019, 90.590, 288.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Thioredoxin 1,Poly(U)-binding-splicing factor PUF60 / Trx-1 / 60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP- ...Trx-1 / 60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP-interacting repressor / Ro-binding protein 1 / RoBP1 / Siah-binding protein 1 / Siah-BP1


Mass: 24671.930 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: human PUF60 UHM domain (thioredoxin fusion)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: trxA, fipA, tsnC, b3781, JW5856, PUF60, FIR, ROBPI, SIAHBP1
Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25, UniProt: Q9UHX1
#2: Chemical
ChemComp-EVU / 4-[2-[4-(aminomethyl)phenyl]phenyl]piperazin-2-one


Mass: 281.352 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H19N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3-1.6M AmSO4, 0.2M potassium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 136075 / % possible obs: 93.2 % / Redundancy: 2.708 % / Biso Wilson estimate: 36.646 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.116 / Χ2: 1.162 / Net I/σ(I): 6.95 / Num. measured all: 774605
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.021.480.8360.715114949740345590.4681.10569.5
2.02-2.161.9030.5831.38251046574433550.640.75393.1
2.16-2.332.9180.4212.612603543399431860.8170.51599.5
2.33-2.553.1990.292412707339827397250.8950.35399.7
2.55-2.853.1880.1836.1411479036155360020.9550.22199.6
2.85-3.293.1270.10110.319825831801314250.9850.12298.8
3.29-4.023.010.0616.737888526914262110.9920.07397.4
4.02-5.672.9670.05220.176002220854202270.9920.06497
5.67-203.1470.03821.393588311552114010.9970.04698.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DXB

3dxb


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.25 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 6962 5.1 %RANDOM
Rwork0.2006 ---
obs0.2033 129056 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.65 Å2 / Biso mean: 39.87 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13086 0 168 696 13950
Biso mean--52.35 40.8 -
Num. residues----1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213486
X-RAY DIFFRACTIONr_angle_refined_deg1.421.62918242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90651682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54824.824680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.315152372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1981548
X-RAY DIFFRACTIONr_chiral_restr0.1030.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210256
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 441 -
Rwork0.326 8842 -
all-9283 -
obs--93.01 %

+
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