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- PDB-4bws: Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. -

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Basic information

Entry
Database: PDB / ID: 4bws
TitleCrystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD.
Components
  • CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2
  • POLYGLUTAMINE-BINDING PROTEIN 1
  • THIOREDOXIN-LIKE PROTEIN 4A
KeywordsTRANSCRIPTION / NEURODEGENERATIVE DISORDERS
Function / homology
Function and homology information


neuronal ribonucleoprotein granule / alternative mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / regulation of dendrite morphogenesis / cellular response to exogenous dsRNA / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / spliceosomal tri-snRNP complex assembly ...neuronal ribonucleoprotein granule / alternative mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / regulation of dendrite morphogenesis / cellular response to exogenous dsRNA / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / spliceosomal tri-snRNP complex assembly / positive regulation of type I interferon production / U5 snRNP / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / positive regulation of defense response to virus by host / activation of innate immune response / mRNA Splicing - Major Pathway / spliceosomal complex / fibrillar center / mRNA splicing, via spliceosome / cytoplasmic stress granule / neuron projection development / double-stranded DNA binding / defense response to virus / transcription coactivator activity / nuclear body / nuclear speck / cell cycle / cell division / innate immune response / lipid binding / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GYF domain / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 ...GYF domain / CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Dna Ligase; domain 1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyglutamine-binding protein 1 / CD2 antigen cytoplasmic tail-binding protein 2 / Thioredoxin-like protein 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMizuguchi, M. / Obita, T. / Serita, T. / Kojima, R. / Morimoto, T. / Nabeshima, Y. / Okazawa, H.
CitationJournal: Nat.Commun. / Year: 2014
Title: Mutations in the Pqbp1 Gene Prevent its Interaction with the Spliceosomal Protein U5-15Kd.
Authors: Mizuguchi, M. / Obita, T. / Serita, T. / Kojima, R. / Nabeshima, Y. / Okazawa, H.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN-LIKE PROTEIN 4A
B: POLYGLUTAMINE-BINDING PROTEIN 1
C: CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2
D: THIOREDOXIN-LIKE PROTEIN 4A
E: POLYGLUTAMINE-BINDING PROTEIN 1
F: CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)58,2046
Polymers58,2046
Non-polymers00
Water28816
1
A: THIOREDOXIN-LIKE PROTEIN 4A
B: POLYGLUTAMINE-BINDING PROTEIN 1
C: CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)29,1023
Polymers29,1023
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: THIOREDOXIN-LIKE PROTEIN 4A
E: POLYGLUTAMINE-BINDING PROTEIN 1
F: CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)29,1023
Polymers29,1023
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.180, 40.470, 168.171
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein THIOREDOXIN-LIKE PROTEIN 4A / DIM1 PROTEIN HOMOLOG / SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN / THIOREDOXIN-LIKE U5 SNRNP ...DIM1 PROTEIN HOMOLOG / SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN / THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD / U5-15KD


Mass: 16743.229 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P83876
#2: Protein/peptide POLYGLUTAMINE-BINDING PROTEIN 1 / PQBP-1 / 38 KDA NUCLEAR PROTEIN CONTAINING A WW DOMAIN / NPW38 / POLYGLUTAMINE TRACT-BINDING ...PQBP-1 / 38 KDA NUCLEAR PROTEIN CONTAINING A WW DOMAIN / NPW38 / POLYGLUTAMINE TRACT-BINDING PROTEIN 1 / PQBP-1


Mass: 3876.208 Da / Num. of mol.: 2 / Fragment: RESIDUES 223-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O60828
#3: Protein CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2 / CD2 CYTOPLASMIC DOMAIN-BINDING PROTEIN 2 / CD2 TAIL-BINDING PROTEIN 2 / U5 SNRNP 52K PROTEIN / U5- ...CD2 CYTOPLASMIC DOMAIN-BINDING PROTEIN 2 / CD2 TAIL-BINDING PROTEIN 2 / U5 SNRNP 52K PROTEIN / U5-52K / U5-52KD


Mass: 8482.363 Da / Num. of mol.: 2 / Fragment: RESIDUES 280-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O95400
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.27 Å / Num. obs: 34203 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 25.28 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYX

1syx


Resolution: 2.5→41.818 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 1732 5.1 %
Rwork0.2379 --
obs0.2399 34180 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→41.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 16 3667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083758
X-RAY DIFFRACTIONf_angle_d1.1925095
X-RAY DIFFRACTIONf_dihedral_angle_d16.6471377
X-RAY DIFFRACTIONf_chiral_restr0.08518
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.35821350.3032662X-RAY DIFFRACTION100
2.5736-2.65660.35231290.29412681X-RAY DIFFRACTION100
2.6566-2.75150.31661440.28732680X-RAY DIFFRACTION100
2.7515-2.86170.37791730.2772636X-RAY DIFFRACTION100
2.8617-2.99190.30481360.27252667X-RAY DIFFRACTION100
2.9919-3.14960.28331130.2622730X-RAY DIFFRACTION100
3.1496-3.34680.31321410.24492705X-RAY DIFFRACTION100
3.3468-3.60510.30671330.24892688X-RAY DIFFRACTION100
3.6051-3.96770.23261360.22252725X-RAY DIFFRACTION100
3.9677-4.54120.23741630.19672712X-RAY DIFFRACTION100
4.5412-5.71910.23061660.19622722X-RAY DIFFRACTION100
5.7191-41.82420.2341630.20732840X-RAY DIFFRACTION100

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