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- PDB-6slo: Crystal structure of PUF60 UHM domain in complex with 7,8 dimetho... -

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Basic information

Entry
Database: PDB / ID: 6slo
TitleCrystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine
ComponentsThioredoxin,Poly(U)-binding-splicing factor PUF60
KeywordsSPLICING / UHM domain / Splicing Inhibitor
Function / homology
Function and homology information


glycerol ether metabolic process / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process ...glycerol ether metabolic process / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / protein-disulfide reductase activity / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. ...Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Thioredoxin-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Chem-LJT / Thioredoxin / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesCitrobacter freundii MGH 56 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJagtap, P.K.A. / Kubelka, T. / Bach, T. / Sattler, M.
CitationJournal: Nat Commun / Year: 2020
Title: Identification of phenothiazine derivatives as UHM-binding inhibitors of early spliceosome assembly.
Authors: Jagtap, P.K.A. / Kubelka, T. / Soni, K. / Will, C.L. / Garg, D. / Sippel, C. / Kapp, T.G. / Potukuchi, H.K. / Schorpp, K. / Hadian, K. / Kessler, H. / Luhrmann, R. / Hausch, F. / Bach, T. / Sattler, M.
History
DepositionAug 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin,Poly(U)-binding-splicing factor PUF60
B: Thioredoxin,Poly(U)-binding-splicing factor PUF60
C: Thioredoxin,Poly(U)-binding-splicing factor PUF60
D: Thioredoxin,Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6648
Polymers98,6884
Non-polymers9774
Water12,070670
1
A: Thioredoxin,Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7213
Polymers24,6721
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin,Poly(U)-binding-splicing factor PUF60


Theoretical massNumber of molelcules
Total (without water)24,6721
Polymers24,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin,Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1362
Polymers24,6721
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin,Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1362
Polymers24,6721
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.520, 89.400, 149.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-804-

HOH

21A-833-

HOH

31B-671-

HOH

41B-695-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 348 through 349 or resid 351...
21(chain B and (resid 348 through 349 or resid 351...
31(chain C and (resid 348 through 349 or resid 351...
41(chain D and (resid 348 through 349 or resid 351...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE(chain A and (resid 348 through 349 or resid 351...AA348 - 34914 - 15
12LEULEUALAALA(chain A and (resid 348 through 349 or resid 351...AA351 - 36317 - 29
13ASPASPASPASP(chain A and (resid 348 through 349 or resid 351...AA36430
14PROPROALAALA(chain A and (resid 348 through 349 or resid 351...AA343 - 5569 - 222
15PROPROALAALA(chain A and (resid 348 through 349 or resid 351...AA343 - 5569 - 222
16PROPROALAALA(chain A and (resid 348 through 349 or resid 351...AA343 - 5569 - 222
17PROPROALAALA(chain A and (resid 348 through 349 or resid 351...AA343 - 5569 - 222
21ILEILEILEILE(chain B and (resid 348 through 349 or resid 351...BB348 - 34914 - 15
22LEULEUALAALA(chain B and (resid 348 through 349 or resid 351...BB351 - 36317 - 29
23ASPASPASPASP(chain B and (resid 348 through 349 or resid 351...BB36430
24PROPROALAALA(chain B and (resid 348 through 349 or resid 351...BB343 - 5569 - 222
25PROPROALAALA(chain B and (resid 348 through 349 or resid 351...BB343 - 5569 - 222
26PROPROALAALA(chain B and (resid 348 through 349 or resid 351...BB343 - 5569 - 222
27PROPROALAALA(chain B and (resid 348 through 349 or resid 351...BB343 - 5569 - 222
31ILEILEILEILE(chain C and (resid 348 through 349 or resid 351...CC348 - 34914 - 15
32LEULEUASPASP(chain C and (resid 348 through 349 or resid 351...CC351 - 39117 - 57
33TYRTYRLYSLYS(chain C and (resid 348 through 349 or resid 351...CC393 - 44459 - 110
34GLUGLUGLUGLU(chain C and (resid 348 through 349 or resid 351...CC445111
35ILEILEALAALA(chain C and (resid 348 through 349 or resid 351...CC348 - 55614 - 222
36ILEILEALAALA(chain C and (resid 348 through 349 or resid 351...CC348 - 55614 - 222
37ILEILEALAALA(chain C and (resid 348 through 349 or resid 351...CC348 - 55614 - 222
38ILEILEALAALA(chain C and (resid 348 through 349 or resid 351...CC348 - 55614 - 222
41ILEILEILEILE(chain D and (resid 348 through 349 or resid 351...DD348 - 34914 - 15
42LEULEUALAALA(chain D and (resid 348 through 349 or resid 351...DD351 - 36317 - 29
43ASPASPASPASP(chain D and (resid 348 through 349 or resid 351...DD36430
44ILEILEALAALA(chain D and (resid 348 through 349 or resid 351...DD348 - 55614 - 222
45ILEILEALAALA(chain D and (resid 348 through 349 or resid 351...DD348 - 55614 - 222
46ILEILEALAALA(chain D and (resid 348 through 349 or resid 351...DD348 - 55614 - 222
47ILEILEALAALA(chain D and (resid 348 through 349 or resid 351...DD348 - 55614 - 222

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Components

#1: Protein
Thioredoxin,Poly(U)-binding-splicing factor PUF60 / 60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP- ...60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP-interacting repressor / Ro-binding protein 1 / RoBP1 / Siah-binding protein 1 / Siah-BP1


Mass: 24671.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii MGH 56 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: AF42_05360, PUF60, FIR, ROBPI, SIAHBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A064CXU8, UniProt: Q9UHX1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LJT / 2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl)propyl]piperazin-1-yl]ethanol


Mass: 464.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30ClN3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O
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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.4M ammonium sulfate, 0.05M K-formate,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0716 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 1.94→55.036 Å / Num. obs: 81211 / % possible obs: 99.8 % / Redundancy: 5.09 % / Biso Wilson estimate: 38.923 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.085 / Χ2: 0.977 / Net I/σ(I): 12.8 / Num. measured all: 413389 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.94-1.995.1070.7992.3630221592859170.7340.88999.8
1.99-2.044.9840.6332.9628904580957990.7860.70699.8
2.04-2.14.6210.4793.6425871560655980.850.54199.9
2.1-2.175.2220.3734.8128609548354790.9230.41499.9
2.17-2.245.3070.2846.1728431536353570.9540.31599.9
2.24-2.325.2810.2287.3427062512651240.9670.253100
2.32-2.415.2490.1878.5926063497649650.9790.20899.8
2.41-2.55.1890.1559.8724805478447800.9840.17299.9
2.5-2.624.9910.12711.423010461346100.9890.14299.9
2.62-2.744.770.10412.9821047441444120.990.117100
2.74-2.895.420.09215.7222768420242010.9940.102100
2.89-3.075.3350.07718.3221190397239720.9940.085100
3.07-3.285.2550.06521.5519729376737540.9950.07299.7
3.28-3.545.1370.05724.4817922350734890.9960.06499.5
3.54-3.884.5910.05225.2214780323532190.9960.05999.5
3.88-4.345.1330.0528.2215071294229360.9960.05699.8
4.34-5.015.2390.04729.5313622260826000.9970.05399.7
5.01-6.135.0180.04828.8911185223422290.9950.05499.8
6.13-8.684.570.04627.858012177017530.9970.05299
8.68-55.0365.0020.04631.285087104110170.9960.05297.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DXB

3dxb


Resolution: 1.94→55.036 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 4061 5 %
Rwork0.176 77144 -
obs0.1776 81205 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.91 Å2 / Biso mean: 43.9395 Å2 / Biso min: 17.52 Å2
Refinement stepCycle: final / Resolution: 1.94→55.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 55 670 7199
Biso mean--48.31 45.74 -
Num. residues----846
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2444X-RAY DIFFRACTION10.596TORSIONAL
12B2444X-RAY DIFFRACTION10.596TORSIONAL
13C2444X-RAY DIFFRACTION10.596TORSIONAL
14D2444X-RAY DIFFRACTION10.596TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.94-1.96270.30621360.27392583100
1.9627-1.98670.28651410.2512683100
1.9867-2.01180.30411350.23292555100
2.0118-2.03830.26211390.23022650100
2.0383-2.06620.22181380.21152613100
2.0662-2.09570.24961390.20022648100
2.0957-2.1270.24291390.20292640100
2.127-2.16030.23121390.19422640100
2.1603-2.19570.24321380.18862627100
2.1957-2.23350.23511400.18642647100
2.2335-2.27420.18931380.18772624100
2.2742-2.31790.21561390.17862658100
2.3179-2.36520.17711390.17252641100
2.3652-2.41660.2361400.17462652100
2.4166-2.47290.22421390.17162639100
2.4729-2.53470.23111390.17312649100
2.5347-2.60320.19951390.17742632100
2.6032-2.67980.22351400.18112661100
2.6798-2.76630.21731400.18152658100
2.7663-2.86520.19881400.18652672100
2.8652-2.97990.22541410.19742664100
2.9799-3.11550.2431400.19142666100
3.1155-3.27980.20821410.18442677100
3.2798-3.48520.22391400.1752266499
3.4852-3.75430.20381410.16252683100
3.7543-4.13190.17581420.14782696100
4.1319-4.72960.16161430.14152712100
4.7296-5.95760.17251450.15482760100
5.9576-55.0360.20341510.1853285099
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)
11.3403-0.011-0.23882.09410.19493.3434-0.0454-0.14410.10340.17220.18080.10780.0351-0.2083-0.13480.1657-0.03940.02340.2444-0.00760.22757.106826.634751.8018
24.2336-0.6608-0.56363.03310.23692.9043-0.05630.2967-0.52610.1862-0.23460.89220.5417-0.72330.31820.5955-0.11860.10070.4309-0.13530.519460.9745-8.65019.3662
30.6653-1.3616-1.44021.07631.68091.6242-0.1290.0874-0.07060.1448-0.14750.13570.5358-0.17560.29980.582-0.08170.0810.3433-0.03920.36162.80660.125420.3826
42.37510.42560.75462.03560.09342.8919-0.09990.51790.2225-0.41360.17680.0323-0.2980.1641-0.12810.2826-0.11410.01390.31150.04940.226656.466126.860822.3797
52.0671-0.10632.27071.9643-0.68273.0354-0.37720.33580.78350.22850.2932-0.4891-0.40890.51990.0510.453-0.23540.10020.4719-0.11940.652383.15741.725929.5328
62.9747-0.1985-0.43891.4870.38672.12440.1079-0.15790.2879-0.24640.2293-0.4279-0.33060.7595-0.20930.2706-0.20070.10160.508-0.12860.450382.035333.607231.321
72.1313-0.2502-0.57421.4443-0.0972.48110.04740.14620.074-0.28320.1572-0.132-0.1310.1977-0.20350.23-0.14320.04380.3018-0.02830.267573.037130.572430.1748
80.2167-0.3391-0.28831.55841.090.56210.018-0.14730.193-0.55780.3282-0.1354-0.00270.4153-0.3220.4150.0010.04580.3529-0.09260.342285.439117.887422.9521
95.1344-0.07850.1042.70470.20613.15140.02021.09950.4344-0.37310.00690.566-0.5475-0.5458-0.02350.55830.1127-0.02870.49190.10530.377570.990911.0208-6.5484
103.54130.8822-0.46461.7844-0.4652.21660.14990.18990.2560.04-0.16440.3014-0.3828-0.1879-0.05890.51950.07830.03270.31640.01730.311573.091110.83991.2562
113.71360.1884-0.05745.2913-0.21981.85980.02390.27650.53520.07580.02020.4921-0.5706-0.29740.01120.60080.09190.02950.29690.04320.33974.199313.84553.6202
121.86290.2398-0.18552.6393-0.02522.96870.1254-0.1182-0.27830.06460.09050.07490.377-0.0784-0.17010.2185-0.0707-0.06620.20570.01760.266151.33973.416842.8287
130.1289-0.2141.69370.0455-0.80865.45440.0355-0.0726-0.01990.0643-0.4185-0.0290.5235-0.1340.51180.3460.0521-0.08690.5262-0.02270.358866.9995-3.435550.4552
141.7077-1.31021.03454.1421-1.48792.6796-0.0429-0.2260.13180.18750.25660.4099-0.5884-0.4788-0.13150.37010.04620.05520.2770.05020.286969.14099.355876.6592
153.7060.7973-0.08144.272-0.37032.67440.16930.18640.0523-0.1570.14480.6266-0.1389-0.5637-0.32340.33710.0213-0.03320.34780.08260.317866.71171.241172.4098
162.9095-1.0470.6322.8321-0.98652.3859-0.09250.50160.875-0.0303-0.1253-0.5001-0.80130.20220.16870.6673-0.07380.05730.35720.10550.493284.062220.966863.905
173.7747-3.11621.38883.9218-2.63192.8151-0.7056-0.4964-0.28990.8080.11-0.01030.270.53840.50920.54350.02780.05080.51230.08780.342877.548820.850148.2466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 460 through 556 )C460 - 556
2X-RAY DIFFRACTION2chain 'D' and (resid 348 through 420 )D348 - 420
3X-RAY DIFFRACTION3chain 'D' and (resid 421 through 459 )D421 - 459
4X-RAY DIFFRACTION4chain 'D' and (resid 460 through 556 )D460 - 556
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 355 )A343 - 355
6X-RAY DIFFRACTION6chain 'A' and (resid 356 through 403 )A356 - 403
7X-RAY DIFFRACTION7chain 'A' and (resid 404 through 439 )A404 - 439
8X-RAY DIFFRACTION8chain 'A' and (resid 440 through 459 )A440 - 459
9X-RAY DIFFRACTION9chain 'A' and (resid 460 through 486 )A460 - 486
10X-RAY DIFFRACTION10chain 'A' and (resid 487 through 529 )A487 - 529
11X-RAY DIFFRACTION11chain 'A' and (resid 530 through 556 )A530 - 556
12X-RAY DIFFRACTION12chain 'B' and (resid 343 through 439 )B343 - 439
13X-RAY DIFFRACTION13chain 'B' and (resid 440 through 459 )B440 - 459
14X-RAY DIFFRACTION14chain 'B' and (resid 460 through 518 )B460 - 518
15X-RAY DIFFRACTION15chain 'B' and (resid 519 through 556 )B519 - 556
16X-RAY DIFFRACTION16chain 'C' and (resid 348 through 439 )C348 - 439
17X-RAY DIFFRACTION17chain 'C' and (resid 440 through 459 )C440 - 459

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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