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- PDB-4pyu: The conserved ubiquitin-like protein hub1 plays a critical role i... -

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Basic information

Entry
Database: PDB / ID: 4pyu
TitleThe conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells
Components
  • U4/U6.U5 tri-snRNP-associated protein 1
  • Ubiquitin-like protein 5
KeywordsPROTEIN BINDING/ALLERGEN / UBIQUITIN-LIKE / PRE-MRNA SPLICING / PROTEIN BINDING-ALLERGEN COMPLEX
Function / homology
Function and homology information


positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / positive regulation of protein targeting to mitochondrion / Cajal body / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway ...positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / positive regulation of protein targeting to mitochondrion / Cajal body / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / protein modification process / protein tag activity / mRNA splicing, via spliceosome / nuclear speck / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like modifier Hub1/Ubl5 / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin-like domain / Ubiquitin-like domain superfamily ...Ubiquitin-like modifier Hub1/Ubl5 / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
U4/U6.U5 tri-snRNP-associated protein 1 / Ubiquitin-like protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAmmon, T. / Mishra, S.K. / Kowalska, K. / Popowicz, G.M. / Holak, T.A. / Jentsch, S.
CitationJournal: J Mol Cell Biol / Year: 2014
Title: The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells.
Authors: Ammon, T. / Mishra, S.K. / Kowalska, K. / Popowicz, G.M. / Holak, T.A. / Jentsch, S.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein 5
B: Ubiquitin-like protein 5
C: U4/U6.U5 tri-snRNP-associated protein 1
D: U4/U6.U5 tri-snRNP-associated protein 1
G: Ubiquitin-like protein 5
H: U4/U6.U5 tri-snRNP-associated protein 1
K: Ubiquitin-like protein 5
L: U4/U6.U5 tri-snRNP-associated protein 1
O: Ubiquitin-like protein 5
P: U4/U6.U5 tri-snRNP-associated protein 1
S: Ubiquitin-like protein 5
T: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)65,74712
Polymers65,74712
Non-polymers00
Water5,170287
1
A: Ubiquitin-like protein 5
C: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area5450 Å2
MethodPISA
2
B: Ubiquitin-like protein 5
D: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area5330 Å2
MethodPISA
3
G: Ubiquitin-like protein 5
H: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area5290 Å2
MethodPISA
4
K: Ubiquitin-like protein 5
L: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area5340 Å2
MethodPISA
5
O: Ubiquitin-like protein 5
P: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8 kcal/mol
Surface area5380 Å2
MethodPISA
6
S: Ubiquitin-like protein 5
T: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)10,9582
Polymers10,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.510, 103.630, 67.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Ubiquitin-like protein 5


Mass: 8843.222 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL5 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9BZL1
#2: Protein/peptide
U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 / U4/U6.U5 tri-snRNP-associated 110 kDa protein


Mass: 2114.529 Da / Num. of mol.: 6 / Fragment: UBL5 BINDING MOTIF (UNP RESIDUES 117-135) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43290
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M TRIS-HCL, 0.15 M SODIUM ACETATE, 20% W/V PEG4000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 41956 / Num. obs: 41837 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.48 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.568 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.217 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1840 5 %RANDOM
Rwork0.186 ---
obs0.189 34641 87 %-
all-41956 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 0 287 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194517
X-RAY DIFFRACTIONr_bond_other_d0.0020.024423
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9656091
X-RAY DIFFRACTIONr_angle_other_deg0.889310168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55525.187187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6115860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.131515
X-RAY DIFFRACTIONr_chiral_restr0.1240.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 96 -
Rwork0.189 1726 -
obs--60.21 %

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