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- PDB-5ctr: Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL... -

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Basic information

Entry
Database: PDB / ID: 5ctr
TitleCrystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL domain complex
Components
  • Squamous cell carcinoma antigen recognized by T-cells 3
  • Ubiquitin carboxyl-terminal hydrolase 4
KeywordsIMMUNE SYSTEM / NUCLEAR PROTEIN / RNA BINDING PROTEIN / HYDROLASE / Nuclear complex / Deubiquitinase
Function / homology
Function and homology information


adenosine receptor binding / U6atac snRNA binding / ASAP complex / regulation of RNA metabolic process / U4 snRNA binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / transcription elongation-coupled chromatin remodeling / hematopoietic stem cell proliferation / ubiquitin-specific protease binding ...adenosine receptor binding / U6atac snRNA binding / ASAP complex / regulation of RNA metabolic process / U4 snRNA binding / protein localization to cell surface / TNFR1-induced proapoptotic signaling / transcription elongation-coupled chromatin remodeling / hematopoietic stem cell proliferation / ubiquitin-specific protease binding / spliceosomal tri-snRNP complex assembly / homeostasis of number of cells / protein deubiquitination / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / mRNA splicing, via spliceosome / regulation of protein stability / cell morphogenesis / nucleosome assembly / regulation of gene expression / protein-macromolecule adaptor activity / histone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / nuclear speck / proteolysis / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / DUSP-like / DUSP-like / LSM-interacting domain / Lsm interaction motif / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / DUSP-like / DUSP-like / LSM-interacting domain / Lsm interaction motif / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / PRP39 C-terminal HAT repeat / PRP39 N-terminal HAT repeat / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Tetratricopeptide repeat domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Roll / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 4 / Spliceosome associated factor 3, U4/U6 recycling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.012 Å
AuthorsPark, J.K. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2011-0021713 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3
Authors: Park, J.K. / Das, T. / Song, E.J. / Kim, E.E.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Squamous cell carcinoma antigen recognized by T-cells 3
B: Squamous cell carcinoma antigen recognized by T-cells 3
C: Ubiquitin carboxyl-terminal hydrolase 4
D: Ubiquitin carboxyl-terminal hydrolase 4


Theoretical massNumber of molelcules
Total (without water)133,8624
Polymers133,8624
Non-polymers00
Water70339
1
A: Squamous cell carcinoma antigen recognized by T-cells 3
C: Ubiquitin carboxyl-terminal hydrolase 4


Theoretical massNumber of molelcules
Total (without water)66,9312
Polymers66,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Squamous cell carcinoma antigen recognized by T-cells 3
D: Ubiquitin carboxyl-terminal hydrolase 4


Theoretical massNumber of molelcules
Total (without water)66,9312
Polymers66,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.202, 115.202, 306.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Squamous cell carcinoma antigen recognized by T-cells 3 / SART-3 / Tat-interacting protein of 110 kDa / Tip110 / p110 nuclear RNA-binding protein


Mass: 39913.336 Da / Num. of mol.: 2 / Fragment: UNP residues 278-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15020
#2: Protein Ubiquitin carboxyl-terminal hydrolase 4 / Deubiquitinating enzyme 4 / Ubiquitin thioesterase 4 / Ubiquitin-specific-processing protease 4 / ...Deubiquitinating enzyme 4 / Ubiquitin thioesterase 4 / Ubiquitin-specific-processing protease 4 / Ubiquitous nuclear protein homolog


Mass: 27017.449 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP4, UNP, UNPH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13107, ubiquitinyl hydrolase 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES pH 6.8, 200 mM magnesium chloride, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 41894 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.26 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTQ

5ctq


Resolution: 3.012→50 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 33.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3337 1999 4.88 %
Rwork0.3088 --
obs0.31 40978 98.11 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.62 Å2 / ksol: 0.247 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4982 Å20 Å20 Å2
2--2.4982 Å20 Å2
3----4.9963 Å2
Refinement stepCycle: LAST / Resolution: 3.012→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8538 0 0 39 8577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068726
X-RAY DIFFRACTIONf_angle_d1.30511818
X-RAY DIFFRACTIONf_dihedral_angle_d15.6163280
X-RAY DIFFRACTIONf_chiral_restr0.0721260
X-RAY DIFFRACTIONf_plane_restr0.0071531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0116-3.08690.58141380.53832685X-RAY DIFFRACTION96
3.0869-3.17030.47751360.48762655X-RAY DIFFRACTION96
3.1703-3.26350.46611380.45392704X-RAY DIFFRACTION97
3.2635-3.36880.41361390.40582707X-RAY DIFFRACTION97
3.3688-3.48910.38481410.35692730X-RAY DIFFRACTION98
3.4891-3.62870.37461410.31682759X-RAY DIFFRACTION98
3.6287-3.79370.31391420.29562771X-RAY DIFFRACTION99
3.7937-3.99350.31891420.26962778X-RAY DIFFRACTION98
3.9935-4.24350.28141430.25892771X-RAY DIFFRACTION99
4.2435-4.57060.29261430.25072800X-RAY DIFFRACTION99
4.5706-5.02960.28491460.25012820X-RAY DIFFRACTION99
5.0296-5.75530.30341450.2762848X-RAY DIFFRACTION99
5.7553-7.2430.32311480.26612895X-RAY DIFFRACTION99
7.243-38.19660.26031570.25513056X-RAY DIFFRACTION99

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