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- PDB-6lur: Human PUF60 UHM domain (thioredoxin fusion) in complex with a sma... -

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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


mRNA splice site recognition / alternative mRNA splicing, via spliceosome / 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 ...mRNA splice site recognition / alternative mRNA splicing, via spliceosome / 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 / cytoplasm / cytosol
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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