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- PDB-3dxb: Structure of the UHM domain of Puf60 fused to thioredoxin -

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Basic information

Entry
Database: PDB / ID: 3dxb
TitleStructure of the UHM domain of Puf60 fused to thioredoxin
Componentsthioredoxin N-terminally fused to Puf60(UHM)
KeywordsSPLICING / TRANSCRIPTION / FBP interacting repressor / UHM / RRM / Electron transport / Redox-active center / Transport
Function / homology
Function and homology information


mRNA splice site recognition / alternative mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding ...mRNA splice site recognition / alternative mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding
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 / Thioredoxin family active 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
Thioredoxin 1 / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCorsini, L. / Hothorn, M. / Scheffzek, K. / Stier, G. / Sattler, M.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Dimerization and Protein Binding Specificity of the U2AF Homology Motif of the Splicing Factor Puf60.
Authors: Corsini, L. / Hothorn, M. / Stier, G. / Rybin, V. / Scheffzek, K. / Gibson, T.J. / Sattler, M.
#1: Journal: Protein Sci. / Year: 2008
Title: Thioredoxin as a fusion tag for carrier-driven crystallization.
Authors: Corsini, L. / Hothorn, M. / Scheffzek, K. / Sattler, M. / Stier, G.
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thioredoxin N-terminally fused to Puf60(UHM)
B: thioredoxin N-terminally fused to Puf60(UHM)
C: thioredoxin N-terminally fused to Puf60(UHM)
D: thioredoxin N-terminally fused to Puf60(UHM)
E: thioredoxin N-terminally fused to Puf60(UHM)
F: thioredoxin N-terminally fused to Puf60(UHM)
G: thioredoxin N-terminally fused to Puf60(UHM)
H: thioredoxin N-terminally fused to Puf60(UHM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,57913
Polymers197,3758
Non-polymers2045
Water21,4561191
1
A: thioredoxin N-terminally fused to Puf60(UHM)
F: thioredoxin N-terminally fused to Puf60(UHM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4154
Polymers49,3442
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thioredoxin N-terminally fused to Puf60(UHM)
D: thioredoxin N-terminally fused to Puf60(UHM)


Theoretical massNumber of molelcules
Total (without water)49,3442
Polymers49,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: thioredoxin N-terminally fused to Puf60(UHM)
G: thioredoxin N-terminally fused to Puf60(UHM)


Theoretical massNumber of molelcules
Total (without water)49,3442
Polymers49,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: thioredoxin N-terminally fused to Puf60(UHM)
H: thioredoxin N-terminally fused to Puf60(UHM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4775
Polymers49,3442
Non-polymers1333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-98 kcal/mol
Surface area72190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.120, 89.430, 299.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
thioredoxin N-terminally fused to Puf60(UHM)


Mass: 24671.930 Da / Num. of mol.: 8
Fragment: Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559
Source method: isolated from a genetically manipulated source
Details: The UHM domain of Puf60 was crystallized as a fusion with E.coli thioredoxin (U niProtKB/Swiss-Prot P0AA27)
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: trxA, Z5291, ECs4714, PUF60,FIR,ROBPI,SIAHBP1 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P0AA27, UniProt: Q9UHX1
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1191 / Source method: isolated from a natural source / Formula: H2O

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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: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.006 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2007
Details: LN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror Beamline suitable for large unit cell structures
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.2→49.832 Å / Num. all: 103128 / Num. obs: 102916 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 36.481 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.106 / Net I/σ(I): 14.53
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.24 / Num. unique all: 16266 / Rsym value: 0.604 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8
Resolution: 2.2→49.75 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 12.772 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.282 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27148 5181 5 %RANDOM
Rwork0.2112 ---
all0.21419 103128 --
obs0.21419 102916 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.623 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---1.26 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13074 0 8 1191 14273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213367
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.96418100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68251702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87426.132623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.816152356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0971548
X-RAY DIFFRACTIONr_chiral_restr0.0660.22046
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210098
X-RAY DIFFRACTIONr_nbd_refined0.1910.26338
X-RAY DIFFRACTIONr_nbtor_refined0.2980.29011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.21296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.224
X-RAY DIFFRACTIONr_mcbond_it0.3411.58719
X-RAY DIFFRACTIONr_mcangle_it0.432213553
X-RAY DIFFRACTIONr_scbond_it0.59735267
X-RAY DIFFRACTIONr_scangle_it0.9214.54547
LS refinement shellResolution: 2.2→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 369 -
Rwork0.26 6924 -
obs--97.57 %

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