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- PDB-8enk: Crystal structure of UAP56 in complex with Tho1, the yeast homolo... -

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Basic information

Entry
Database: PDB / ID: 8enk
TitleCrystal structure of UAP56 in complex with Tho1, the yeast homolog of human SARNP
Components
  • Protein THO1
  • RNA
  • Spliceosome RNA helicase DDX39B
KeywordsRNA BINDING PROTEIN/RNA / mRNA nuclear export / DEAD-box ATPase / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


transcription export complex / U6 snRNP / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / ATP-dependent protein binding / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / U4 snRNP ...transcription export complex / U6 snRNP / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / ATP-dependent protein binding / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / U4 snRNP / poly(A)+ mRNA export from nucleus / spliceosomal complex assembly / U6 snRNA binding / RHOBTB2 GTPase cycle / mRNA export from nucleus / protein-RNA complex assembly / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / double-stranded DNA binding / RNA helicase activity / nuclear speck / RNA helicase / mRNA binding / chromatin binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
THO1_MOS11, C-terminal domain / Tho1/MOS11 C-terminal domain / : / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. ...THO1_MOS11, C-terminal domain / Tho1/MOS11 C-terminal domain / : / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / Protein THO1 / Spliceosome RNA helicase DDX39B
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXie, Y. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell Rep / Year: 2023
Title: Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly.
Authors: Xie, Y. / Gao, S. / Zhang, K. / Bhat, P. / Clarke, B.P. / Batten, K. / Mei, M. / Gazzara, M. / Shay, J.W. / Lynch, K.W. / Angelos, A.E. / Hill, P.S. / Ivey, A.L. / Fontoura, B. / Ren, Y.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spliceosome RNA helicase DDX39B
B: Spliceosome RNA helicase DDX39B
E: Protein THO1
M: RNA
N: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,71611
Polymers105,6815
Non-polymers1,0356
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.534, 96.786, 126.180
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

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Components

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Protein , 2 types, 3 molecules ABE

#1: Protein Spliceosome RNA helicase DDX39B / 56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B- ...56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B-associated transcript 1 protein


Mass: 44904.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13838, RNA helicase
#2: Protein Protein THO1


Mass: 6775.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: THO1, YER063W / Production host: Escherichia coli (E. coli) / References: UniProt: P40040

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RNA chain , 1 types, 2 molecules MN

#3: RNA chain RNA


Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 23 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.025 M HEPES, pH 7.4, 0.2 M sodium chloride, and 18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 38274 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 57.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Net I/σ(I): 28.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1873 / CC1/2: 0.799 / Rpim(I) all: 0.396

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTJ

1xtj


Resolution: 2.5→29.72 Å / SU ML: 0.3438 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.2832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 1993 5.23 %
Rwork0.2238 36114 -
obs0.2253 38107 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 220 64 17 6879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336994
X-RAY DIFFRACTIONf_angle_d0.69549460
X-RAY DIFFRACTIONf_chiral_restr0.04481071
X-RAY DIFFRACTIONf_plane_restr0.00451185
X-RAY DIFFRACTIONf_dihedral_angle_d17.08182730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.34931410.31872558X-RAY DIFFRACTION99.96
2.56-2.630.34361400.30712542X-RAY DIFFRACTION99.93
2.63-2.710.29051390.30252536X-RAY DIFFRACTION99.96
2.71-2.80.34631420.30032560X-RAY DIFFRACTION99.96
2.8-2.90.33591400.31052549X-RAY DIFFRACTION99.96
2.9-3.010.34781420.31052565X-RAY DIFFRACTION99.96
3.01-3.150.341410.29932551X-RAY DIFFRACTION100
3.15-3.310.31091420.27982568X-RAY DIFFRACTION99.93
3.32-3.520.30011410.25832561X-RAY DIFFRACTION100
3.52-3.790.27351440.22882584X-RAY DIFFRACTION99.93
3.79-4.170.24551430.20652598X-RAY DIFFRACTION100
4.17-4.780.18311430.1692600X-RAY DIFFRACTION99.96
4.78-6.010.21231460.18862647X-RAY DIFFRACTION99.96
6.01-29.720.20681490.17572695X-RAY DIFFRACTION97.63
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)
11.735469440570.365278088994-0.9816394277193.63840135036-1.00040555441.859950242820.10505489385-0.141080155628-0.255792832940.428748121024-0.549053772814-1.322941101870.6855918511271.65462014410.2971376657810.8101643227070.183553761612-0.2606725415381.073431879020.2121915760750.9345956715635.45437451005-53.733493022570.0423079922
22.654484183830.472729183661-0.2158864400483.31063677036-1.105221798143.033189914510.0747377383816-0.339316146982-0.2534880429560.323039306087-0.253038255209-0.3399067017490.4531810129130.5185427700820.1780168240480.5417675611580.0676881698881-0.1304864321860.4946556816260.08804519423110.507012537208-8.86011419078-51.649479069766.4718287979
32.679864134430.476098681403-0.7424498731263.72029655786-0.45309200542.84405203434-0.0411988403208-0.267068625218-0.09685842367550.191712195143-0.01900981714780.1580702649590.16336222553-0.1801374353410.03371589614210.537395761525-0.0104765571741-0.1075133656780.5318598688430.04247391181540.49097920403-21.5337332217-48.431240441366.9461978756
42.113725089970.4764921550641.093267880121.97370727751-0.5009561016584.56122287602-0.05757484432920.2603762590720.2881471445490.0471391622229-0.224441329268-0.307881440022-0.2503348969890.6738817463190.2311903170780.4040530249020.0191481159723-0.08876796753170.5407488439910.08668514259910.514877440017-6.97876308684-32.866245921747.3019058787
52.902701411471.36710570019-1.0630229211.51341276443-1.819522879853.17224096923-0.05153436304050.119029689395-0.316414408262-0.163578528835-0.149213659365-0.4415218791770.2372955867010.3927119688260.1854122040420.445026023960.082871391902-0.05451266758990.5696076525290.07295995044040.509044502383-7.76001862255-41.657395465747.0874135657
63.140911101261.05520975332-0.3996991076993.23101219593-0.9522598755263.98746149048-0.008776422929190.1379876787590.3580797607370.167525598205-0.378446915492-0.252312209534-0.8790708978360.8932875066210.3187895774730.653079571739-0.132274599855-0.2243478674320.6578720804970.1232316874220.622743427611-2.33161040211-26.305824046952.3628198909
73.768282088351.00714344012-1.700213318331.62465113945-1.859158659214.39565545395-0.284402167929-0.0763574231122-0.164223842308-0.1202058179-0.25808442661-0.5503169196260.4248276521350.3772553178370.5167650385330.48930991972-0.1000648121050.07421224570360.4370785846070.06629490430970.50236437111422.0674845681-25.7142930418-28.8892531802
82.886153095950.973871671466-1.220140440281.53909564728-0.7394415054374.04368706762-0.008276753065860.5767179171980.113614170066-0.2218649820990.2145884910380.2596598163060.181857368048-1.24281171026-0.153312867510.485415065257-0.1478271994880.01181395712120.7778470291950.04948463174760.4987395324461.47445234247-23.5405445892-28.9799269747
91.842233088530.313185128508-0.95073939152.51731558374-1.019013352944.67355441405-0.6013154228350.630489463429-0.463295399305-0.7090711542530.2563969427020.1365021581.10700860086-0.6327434930870.3234165602230.92270192675-0.2875503228470.09033280702430.671801694957-0.1112813274260.6359002872867.95825865739-37.9250126938-36.5166176872
101.383069847680.3911409299760.01267920644240.188718650822-0.2226322203271.929580271940.00552353730336-0.674213002774-1.021162315460.14408131446-0.525036877855-0.2445741082050.241721656520.37236782540.4718131217040.935790410581-0.05377037318270.1423470956430.6300704976150.1879311781750.88819523194114.298054814-48.5838322655-3.90966087543
113.62438392355-0.753874992151-0.5483404366611.58726155051-1.218365761145.68398743533-0.181288504826-0.044492775779-0.181710099960.195206597849-0.1625630424710.0151226632730.180561472433-0.2847319012750.2960329869010.645402125775-0.2329959180330.1074090724240.4966906803620.004210590434950.584217910393.72715546326-37.5405017359-7.47183090003
121.56289561647-0.946896854239-0.7727498856522.44070494427-0.01535645018941.22075282153-0.256803519698-0.48662226415-0.6707157382960.169708525832-0.0587045686733-0.4028017722690.6416701156940.9555214047790.2842583139340.9418731479170.04537962603030.2426128287640.7293136132670.2548728252840.88527831900817.5082875013-48.1710796675-9.70120665988
132.24400812528-1.0346058003-0.509815848422.63016084518-0.1596186338363.42269738699-0.0429407674704-0.9483351461570.05875798786430.138355810180.5779259989630.366309258939-0.07615274325740.284356267155-0.7446222162880.4469762863750.0143306803964-0.008898788906910.7971606013310.006241731593140.5709817647573.08950029742-31.487443800222.0382890946
140.517392005932-0.424656509092-0.308188613390.4072946856820.2269222962163.02996755073-0.50241510670.274963672786-0.530697191649-0.2784858477920.325263230123-0.2952856379830.2988439203080.4752251706040.08420830426940.6425583361510.03533208724930.1471018112410.99408586920.1627377867330.7584851130636.24412429516-41.076734073819.1240177126
150.680777420185-0.6084916585170.6868706138531.831125692790.1725316603681.16778345213-0.04891289669340.34898481039-0.2822353580820.6253592284920.02442973727450.63311300140.0311688553358-0.146262773239-0.007489545241981.04456589441-0.2393304461920.2184729063511.02401873894-0.0795899223840.78924878886-3.2870687789-33.544119768910.6294445131
165.793313441571.72702553836-1.653333534763.63457385723-0.5918730323624.919492756210.2386712041830.3821610962270.6739701178310.250706702742-0.3034372619590.74980887116-0.661710923382-0.623405810916-0.1712682240240.6966093564980.0191671928158-0.117112293960.720660781220.004940592092330.583867796279-25.1321290416-41.300938137152.1396587667
173.52069094530.591388965804-2.456353628495.03293862186-0.2921902106994.567986762630.03971817582361.31738197561-1.00475288483-0.420097911115-0.2990812983750.3863925363361.87985374596-1.443357478910.4631620335050.968174550525-0.4342810057020.04171155331421.15965071225-0.04410567598430.740705201025-6.1510441569-39.9616033134-23.6314477834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 46 through 69 )AA46 - 691 - 24
22chain 'A' and (resid 70 through 153 )AA70 - 15325 - 108
33chain 'A' and (resid 154 through 242 )AA154 - 242109 - 197
44chain 'A' and (resid 243 through 322 )AA243 - 322198 - 277
55chain 'A' and (resid 323 through 367 )AA323 - 367278 - 322
66chain 'A' and (resid 368 through 424 )AA368 - 424323 - 379
77chain 'B' and (resid 44 through 106 )BE44 - 1061 - 63
88chain 'B' and (resid 107 through 181 )BE107 - 18164 - 138
99chain 'B' and (resid 182 through 253 )BE182 - 253139 - 210
1010chain 'B' and (resid 254 through 284 )BE254 - 284211 - 241
1111chain 'B' and (resid 285 through 367 )BE285 - 367242 - 324
1212chain 'B' and (resid 368 through 424 )BE368 - 424325 - 381
1313chain 'E' and (resid 123 through 142 )EI123 - 1421 - 20
1414chain 'E' and (resid 143 through 162 )EI143 - 16221 - 40
1515chain 'E' and (resid 163 through 175 )EI163 - 17541 - 53
1616chain 'M' and (resid 1 through 6 )MJ1 - 6
1717chain 'N' and (resid 2 through 6 )NK2 - 6

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