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- PDB-8id2: Crystal structure of the ubiquitin-like domain in the SF3A1 subun... -

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Basic information

Entry
Database: PDB / ID: 8id2
TitleCrystal structure of the ubiquitin-like domain in the SF3A1 subunit of human U2 snRNP complexed with the stem-loop 4 of U1 snRNA
Components
  • RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*CP*GP*UP*UP*CP*GP*CP*GP*CP*UP*UP*UP*CP*CP*CP*C)-3')
  • Splicing factor 3A subunit 1
KeywordsRNA BINDING PROTEIN/RNA / Splicing / UNCG tetraloop / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex ...U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Ubiquitin family ...Splicing factor 3A subunit 1, ubiquitin domain / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Splicing factor 3A subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTerawaki, S. / Nameki, N. / Kuwasako, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K06105 Japan
Other privateThe Asahi Glass Foundation
CitationJournal: J.Biochem. / Year: 2023
Title: Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP.
Authors: Nameki, N. / Terawaki, S.I. / Takizawa, M. / Kitamura, M. / Muto, Y. / Kuwasako, K.
History
DepositionFeb 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Splicing factor 3A subunit 1
B: Splicing factor 3A subunit 1
C: RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*CP*GP*UP*UP*CP*GP*CP*GP*CP*UP*UP*UP*CP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*CP*GP*UP*UP*CP*GP*CP*GP*CP*UP*UP*UP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,3814
Polymers41,3814
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.455, 60.214, 103.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 703 through 788)
d_2ens_1(chain "B" and resid 703 through 788)
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYARGARGAA703 - 78827 - 112
d_2ens_1GLYGLYARGARGBB703 - 78827 - 112
d_1ens_2GGCCCC1 - 241 - 24
d_2ens_2GGCCDD1 - 241 - 24

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.891180639062, 0.0655653551588, 0.44888556756), (0.112745796536, -0.990465071859, -0.0791664499105), (0.439414899525, 0.121161568292, -0.8900755139)-19.388584282, 88.7669166291, 66.8653306952
2given(0.769411693052, -0.0115890542397, 0.638648056771), (-0.03896958464, -0.998824591121, 0.0288237340391), (0.637563344358, -0.0470651675106, -0.768958940346)-22.2806041786, 87.9627069168, 63.7175112549

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Components

#1: Protein Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 13061.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3A1, SAP114 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15459
#2: RNA chain RNA (5'-R(*GP*GP*GP*GP*AP*CP*UP*GP*CP*GP*UP*UP*CP*GP*CP*GP*CP*UP*UP*UP*CP*CP*CP*C)-3')


Mass: 7629.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM MIB buffer (pH 5.0), 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.8→40.39 Å / Num. obs: 32309 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 46.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.4 % / Rmerge(I) obs: 4.198 / Num. unique obs: 1809 / CC1/2: 0.458 / Rpim(I) all: 1.604 / Rrim(I) all: 4.362 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40.39 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.5938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 1997 6.23 %
Rwork0.1938 30043 -
obs0.1965 32040 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 1006 0 100 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962578
X-RAY DIFFRACTIONf_angle_d1.25353708
X-RAY DIFFRACTIONf_chiral_restr0.0638462
X-RAY DIFFRACTIONf_plane_restr0.0085297
X-RAY DIFFRACTIONf_dihedral_angle_d13.51641118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.536634655388
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.09766182527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.851301942X-RAY DIFFRACTION91.08
1.85-1.90.40311400.37152106X-RAY DIFFRACTION99.16
1.9-1.950.37681400.33492123X-RAY DIFFRACTION99.52
1.95-2.010.35141420.31632121X-RAY DIFFRACTION99.69
2.01-2.090.35811420.27742143X-RAY DIFFRACTION99.52
2.09-2.170.31321410.26632117X-RAY DIFFRACTION99.82
2.17-2.270.30141410.24582155X-RAY DIFFRACTION99.87
2.27-2.390.32991440.252153X-RAY DIFFRACTION99.83
2.39-2.540.31421420.25452148X-RAY DIFFRACTION99.83
2.54-2.730.31211450.26122166X-RAY DIFFRACTION100
2.73-3.010.25341440.23952166X-RAY DIFFRACTION99.48
3.01-3.440.24451440.1952158X-RAY DIFFRACTION99.7
3.44-4.340.20411480.15562215X-RAY DIFFRACTION99.96
4.34-40.390.17781540.14562330X-RAY DIFFRACTION99.84
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)
16.87174608627-2.086537290990.8552795491586.806913981073.695005154165.350685447920.5356502301860.2207584156910.449459520293-1.128234084-0.335208727469-0.780344445326-0.5797162021050.355645605319-0.2324886656030.6494207264010.03723386830030.1342286665980.5133599492520.1522121562630.5792858177953.7179315342383.297160900648.3793843307
27.977908416342.61112558014-0.3294665434812.0814624092-2.440076098539.455449404470.09256794142550.2707786916910.672160716704-0.4834727437760.2005883571640.914646483926-0.4139510599310.120965140367-0.306367623230.4355965704310.0481795378224-0.004786290014040.4204746090820.04318382524920.3699900690530.010554063166481.362366062552.0825446077
33.968213652841.78016735732-2.269663532242.64310554755-3.32436203474.16270010610.3914467258460.1599272477470.516503966510.1859600404610.213471664037-0.118421609407-0.416792360658-0.114300166483-0.6056365011470.6322028282470.0284131669153-0.003645011755310.4777833439490.001179728010650.7976578680495.1613898149537.730716578329.7786436663
44.48400189951.24619320597-2.044485576415.5681901455-3.872432625374.916540685870.138453821592-0.02889147042370.293531434497-0.06049681675410.00020122961143-0.0852312761403-0.0935539237363-0.135429454036-0.1559062492430.4157700647570.0138202734201-0.05082777133280.398672055305-0.05969292169290.46881168281811.454382419422.337774556131.7541012666
57.98060714165-6.272261207471.166225568624.96866833065-1.20121122691.88782411247-0.003841838368970.5907673085611.04403213469-0.0193598710342-0.199665155445-1.84189760113-0.0005086116738160.3181438311090.2843520497570.748762939594-0.08358902897840.07913665480250.482991859920.04288682581041.1665279871911.509057038743.432078564628.0611000787
65.783050890541.856901247611.115527779324.85228469373-1.325489985494.691485379790.0948666645338-0.3976913930150.725440639691-0.0561986214396-0.431650742-0.601724654026-0.379704592188-0.2601374397250.3137419357690.767687384719-0.0966632190471-0.06346562909750.449728209277-0.1298409244910.7197005707390.94180223631452.079997182342.1730937207
71.91953120052.698086841962.309217998458.564251047862.444526173432.888370456230.3593622913990.267173591021-0.5368673589790.756510504921-0.341953791313-0.5672097892590.5390674354520.00717896561378-0.05777982011210.7580281544810.11764037889-0.03587349872350.582763943655-0.189435553540.7753882051078.5428272653464.565814219351.1533037914
83.708480219072.806858721430.7951165154462.231596035221.027588629558.00560602803-0.1609127575650.4824295488640.03858751388650.543928603631-0.08682012194650.9695999163151.07583826409-0.715364820260.3567561648950.543309700154-0.04628310102330.1215176615180.52102247989-0.01773166558260.6548346823530.2219296520972.345251207340.5771290377
97.801087343376.29771828783.670032334746.626268048062.59708370355.121035849630.54425413173-0.339568181912-0.6976761142811.14760741772-0.0595157406747-1.980027728340.177504449390.0869474682089-0.4449002407450.7190307367580.0869047849158-0.1652034070190.464693102164-0.1862200290090.8288240610367.4598412981653.583452588946.0250398518
104.08415886916-4.648003317214.137850110615.2879329004-4.64155983934.310427189031.304097258380.118895342516-1.73104957337-1.16859438018-1.452632607251.593652700831.749316668530.08578748060220.200932015780.8926509060440.221400294674-0.05613271471950.7360022772220.1025217254820.8504436995121.7523952333-13.625814390819.2900243117
117.0467969977-4.478284152860.4077526913858.28701063582-1.145293285775.523142509570.4263186331170.693405260040.406660044164-1.58486592856-0.2530306259380.4201969341-0.55055777339-0.162281510212-0.1391234365920.5869952000220.052245620236-0.02011624899030.515052771270.05938737882120.36739707463410.576218103914.424351434611.0525180006
122.89525735254-0.738571718497-2.809999820718.13956174852-3.025910412974.55554339782-0.0711353437897-0.2336361618710.442777033627-0.148254228254-0.590830297381-1.77800466095-0.007764948696110.3578554643970.6012131967480.3817320781080.0480357872335-0.04479553365150.4294871921940.0330275875360.61986707261718.32689880171.1844349604517.2682132143
132.068555635080.3573595348960.08539720545623.4959000755-5.357178142498.435125686420.2235075110520.359110278820.1722215903160.304484501412-0.650046048097-1.46212408736-0.5038958909311.319563148690.4180727094120.407031795786-0.083501783621-0.03942751966020.5615716968260.1251311728890.67497177062819.31652724310.114306046517.1554622363
149.227816317381.49266434096-2.445376011338.94874182312-4.576006370929.16749494877-0.05588303556550.1835147234160.7868767541020.7177426084-0.114678048114-0.102825464335-0.9093641565220.3505090937060.2169040330830.544502954699-0.145931762693-0.08108371448280.4368500424750.03951455749610.41075405240212.541983888513.063006491420.9047720531
156.31535623424-4.41923434223-1.059721220735.15498513273-2.571208507985.54513383237-0.190547469605-0.167770649666-0.612388537280.426879448768-0.00488112375706-0.1867508996360.0785958063867-0.08332306040040.1825033055680.524714040309-0.0677340612051-0.08136039731820.4289027031780.007430702786660.48571964440810.93739151413.2456000794823.9274576331
168.84901627683-3.39772764715-5.365214457583.303035932455.508998928149.29283461889-0.568693234468-0.4650995524831.44116154124-0.1661751664340.624026905811.22214170194-1.117837309530.228567009071-0.1298417219560.898947935835-0.0384155453078-0.1529853457450.4208787327390.1241021402350.7936552865898.5539984399727.524853014731.3406291768
175.612505383152.089534046982.420677015871.612271183850.8668920285854.74853707373-0.2201802228880.1610605351761.938179333240.2677406715070.362805009420.904598899346-1.239026608480.374002397029-0.1486149154420.724151326461-0.04721919051690.09149529105740.528640725216-0.005001537635651.07439116807-0.065752391664791.186140424559.5351465445
188.815249355012.11754835877-0.6655107149624.55159243982-5.235221006276.454248743890.2041648952190.0135997758551-0.09500190871470.44838990915-0.1595398717240.6735594467420.266727503764-0.334574689134-0.107196217220.476786021683-0.002716227340750.08161006018480.469449907674-0.03802147329670.41921688652-4.5153636240370.323549025964.7055349922
193.833168181944.59146934165-3.976180832655.69172700255-4.465591193259.198133001590.213718895067-0.1218569168460.7724480558660.275407537265-0.350370799956-0.145916228797-1.356756118251.010834019330.2050936472770.759384910983-0.09127374588810.1007344404620.548497921184-0.01031777000360.7601143488824.7289517675288.405582891259.7038075631
208.918618398425.10677299662-4.910515041795.16069988038-5.0465807314.966869663480.443495804792-0.7448200208940.3788002426220.876983354353-0.713743281093-1.12700318868-0.8090467613951.022142032230.2361558516960.414708417519-0.0278978241228-0.000295750551180.461713495625-0.08872709475140.4521089323826.2430529070379.602744287161.3851874947
217.25554658673-0.685080618567-2.026842050525.901893179490.1337249197057.942972011680.1113789716550.342976478189-0.168389879234-0.6662332917480.292543943470.189410740656-0.1157635906470.0370269562919-0.37471751960.3562972926790.032214629128-0.01250478438480.435688123619-0.01809467512990.3205068751512.0626039454775.52652653955.338366766
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 760 through 770 )BB760 - 77060 - 70
22chain 'B' and (resid 771 through 789 )BB771 - 78971 - 89
33chain 'C' and (resid 1 through 5 )CC1 - 5
44chain 'C' and (resid 6 through 20 )CC6 - 20
55chain 'C' and (resid 21 through 24 )CC21 - 24
66chain 'D' and (resid 1 through 5 )DD1 - 5
77chain 'D' and (resid 6 through 10 )DD6 - 10
88chain 'D' and (resid 11 through 15 )DD11 - 15
99chain 'D' and (resid 16 through 24 )DD16 - 24
1010chain 'A' and (resid 699 through 704 )AA699 - 7041 - 6
1111chain 'A' and (resid 705 through 725 )AA705 - 7257 - 27
1212chain 'A' and (resid 726 through 736 )AA726 - 73628 - 38
1313chain 'A' and (resid 737 through 748 )AA737 - 74839 - 50
1414chain 'A' and (resid 749 through 759 )AA749 - 75951 - 61
1515chain 'A' and (resid 760 through 785 )AA760 - 78562 - 87
1616chain 'A' and (resid 786 through 793 )AA786 - 79388 - 95
1717chain 'B' and (resid 701 through 710 )BB701 - 7101 - 10
1818chain 'B' and (resid 711 through 725 )BB711 - 72511 - 25
1919chain 'B' and (resid 726 through 736 )BB726 - 73626 - 36
2020chain 'B' and (resid 737 through 748 )BB737 - 74837 - 48
2121chain 'B' and (resid 749 through 759 )BB749 - 75949 - 59

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