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- PDB-5jjw: Crystal structure of the HAT domain of sart3 in complex with USP1... -

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Basic information

Entry
Database: PDB / ID: 5jjw
TitleCrystal structure of the HAT domain of sart3 in complex with USP15 DUSP-UBL domain
Components
  • Squamous cell carcinoma antigen recognized by T-cells 3
  • Ubiquitin carboxyl-terminal hydrolase 15
KeywordsRNA-binding protein/HYDROLASE / SART3 / HAT / DUSP-UBL / Structural Genomics / Structural Genomics Consortium / SGC / RNA-binding protein-HYDROLASE complex
Function / homology
Function and homology information


U6atac snRNA binding / ASAP complex / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding ...U6atac snRNA binding / ASAP complex / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / U4 snRNA binding / K48-linked deubiquitinase activity / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / protein deubiquitination / SMAD binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / BMP signaling pathway / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / mRNA splicing, via spliceosome / UCH proteinases / nucleosome assembly / histone binding / regulation of gene expression / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / nuclear speck / cysteine-type endopeptidase activity / mitochondrion / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / 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 ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / 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. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / 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 / Tetratricopeptide-like helical domain superfamily / Ubiquitin-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Squamous cell carcinoma antigen recognized by T-cells 3 / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.01 Å
AuthorsDong, A. / Zhang, Q. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the HAT domain of sart3 in complex with USP15 DUSP-UBL domain
Authors: Zhang, Q. / Dong, A. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references

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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: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1634
Polymers62,1012
Non-polymers622
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.925, 117.925, 205.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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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: 35934.547 Da / Num. of mol.: 1 / Fragment: UNP residues 280-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q15020
#2: Protein Ubiquitin carboxyl-terminal hydrolase 15 / Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 ...Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Unph-2 / Unph4


Mass: 26166.576 Da / Num. of mol.: 1 / Fragment: UNP residues 1-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#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: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19% PEG 3350, 0.2 M MgCl2, 0.1 M HEPES pH7.5, 5% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 17447 / % possible obs: 100 % / Redundancy: 30.9 % / Biso Wilson estimate: 96.24 Å2 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.036 / Rrim(I) all: 0.201 / Χ2: 1.094 / Net I/av σ(I): 24.636 / Net I/σ(I): 4 / Num. measured all: 539429
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.0531.62.5941100
3.05-3.1131.51.9991100
3.11-3.1731.71.7531100
3.17-3.2331.81.5031100
3.23-3.331.51.2191100
3.3-3.3831.70.9791100
3.38-3.4631.50.7831100
3.46-3.5631.70.6351100
3.56-3.6631.40.4591100
3.66-3.7831.60.4121100
3.78-3.9131.20.3541100
3.91-4.0731.40.2811100
4.07-4.2631.20.2191100
4.26-4.4831.20.1911100
4.48-4.76310.1631100
4.76-5.1330.80.1491100
5.13-5.6430.60.1281100
5.64-6.4630.10.1221100
6.46-8.1329.60.091100
8.13-5026.50.058199.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.01→44.67 Å / Cor.coef. Fo:Fc: 0.9067 / Cor.coef. Fo:Fc free: 0.8521 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.699 / SU Rfree Blow DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 895 5.15 %RANDOM
Rwork0.2339 ---
obs0.2367 17386 99.87 %-
Displacement parametersBiso max: 224.78 Å2 / Biso mean: 90.45 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.2876 Å20 Å20 Å2
2--1.2876 Å20 Å2
3----2.5751 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: final / Resolution: 3.01→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 5 11 3406
Biso mean--55.81 62.43 -
Num. residues----445
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1352SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1022HARMONIC5
X-RAY DIFFRACTIONt_it6433HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion460SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6966SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6433HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11484HARMONIC2.20.9
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion17.43
LS refinement shellResolution: 3.01→3.19 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.303 142 5.18 %
Rwork0.2633 2600 -
all0.2654 2742 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.6641.4848-3.5645-0.758-3.44380-0.4307-0.3076-0.49150.84790.40280.3487-0.05350.17250.028-0.33160.2240.0455-0.2853-0.07240.1504-23.708447.461634.8201
210.0623-1.1545-2.56514.9121-2.52480-0.1935-0.03060.26760.05440.1019-0.2231-0.0757-0.33420.0917-0.28190.251-0.2052-0.0499-0.26580.1778-11.702951.854334.2414
35.24861.3858-3.08531.2708-2.2942.2531-0.335-0.20591.1927-0.51330.38010.96150.3675-0.1214-0.0452-0.2410.1333-0.4167-0.2089-0.20450.0886-3.202563.823721.033
4-0.2592-1.290710.02545.2488-7.4028.41660.11510.10010.3526-0.8850.1309-0.07110.5192-0.1651-0.2460.14430.0082-0.4119-0.1425-0.0641-0.257311.941763.884.687
52.8294-0.2039-2.87131.9663-1.08560.7045-0.024-0.37480.8881-0.35670.32280.0450.30660.2432-0.2987-0.15830.102-0.3529-0.0888-0.20860.116116.679474.582314.6481
66.14081.54851.1342.6584-4.85183.4479-0.2482-0.06490.8267-0.89860.35690.06170.55440.3646-0.10870.01080.1953-0.2887-0.0621-0.1718-0.276226.859265.005111.7074
77.0732-1.9241.19433.8963-4.34820-0.6649-1.06850.0043-0.26510.18510.28190.27810.08140.47970.03610.3752-0.05870.0068-0.0347-0.448437.445456.984816.8766
89.8615-6.2225-5.79134.33674.61310-0.5119-0.70140.2145-0.23730.2667-0.58330.3711-0.15270.24520.13650.25830.16460.07880.1681-0.125448.985251.757117.163
910.9047-3.28086.2762.3012-4.46848.1685-0.38280.43730.5885-0.1020.4691-0.0040.30940.5897-0.0863-0.1368-0.2083-0.22560.00750.1833-0.220328.029375.9822-11.694
105.75440.25131.76164.70830.60934.0979-0.29490.72551.7299-0.3867-0.1005-0.4127-0.40960.51530.3953-0.1564-0.2872-0.4025-0.1120.35020.14525.062182.8658-10.9307
11-3.19731.92430.86687.21647.88550.0019-0.3336-0.17530.72330.3160.28750.1481-0.41721.63370.0461-0.1858-0.0026-0.41020.3516-0.02280.073242.872877.28879.1233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|280 - 308 }A280 - 308
2X-RAY DIFFRACTION2{ A|309 - 324 }A309 - 324
3X-RAY DIFFRACTION3{ A|325 - 421 }A325 - 421
4X-RAY DIFFRACTION4{ A|422 - 440 }A422 - 440
5X-RAY DIFFRACTION5{ A|441 - 469 }A441 - 469
6X-RAY DIFFRACTION6{ A|470 - 506 }A470 - 506
7X-RAY DIFFRACTION7{ A|507 - 551 }A507 - 551
8X-RAY DIFFRACTION8{ A|552 - 575 }A552 - 575
9X-RAY DIFFRACTION9{ B|6 - 41 }B6 - 41
10X-RAY DIFFRACTION10{ B|42 - 117 }B42 - 117
11X-RAY DIFFRACTION11{ B|118 - 204 }B118 - 204

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