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- PDB-6n3f: Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound ... -

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Basic information

Entry
Database: PDB / ID: 6n3f
TitleStructure of HIV Tat-specific factor 1 U2AF Homology Motif bound to SF3b1 ULM5
Components
  • HIV Tat-specific factor 1
  • SF3b1 U2AF ligand motif
KeywordsPEPTIDE BINDING PROTEIN / HIV Tat-specific factor 1 / TAT-SF1 / RNA SPLICING FACTOR / U2AF HOMOLOGY MOTIF / UHM / RNA BINDING PROTEIN / U2AF LIGAND MOTIF / ULM / PROTEIN-PEPTIDE COMPLEX / PRE-MRNA SPLICING FACTOR / Sf3b1
Function / homology
Function and homology information


U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / protein localization to site of double-strand break / splicing factor binding / U12-type spliceosomal complex / poly-ADP-D-ribose modification-dependent protein binding / : / RNA splicing, via transesterification reactions / U2-type spliceosomal complex ...U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / protein localization to site of double-strand break / splicing factor binding / U12-type spliceosomal complex / poly-ADP-D-ribose modification-dependent protein binding / : / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / double-strand break repair via homologous recombination / spliceosomal complex / B-WICH complex positively regulates rRNA expression / mRNA splicing, via spliceosome / site of double-strand break / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
TatSF1-like, RNA recognition motif 1 / TatSF1-like / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...TatSF1-like, RNA recognition motif 1 / TatSF1-like / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 17S U2 SnRNP complex component HTATSF1 / Splicing factor 3B subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.099 Å
AuthorsLeach, J.R. / Jenkins, J.L. / Kielkopf, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM117005 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM070503 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.
Authors: Loerch, S. / Leach, J.R. / Horner, S.W. / Maji, D. / Jenkins, J.L. / Pulvino, M.J. / Kielkopf, C.L.
History
DepositionNov 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV Tat-specific factor 1
C: HIV Tat-specific factor 1
D: SF3b1 U2AF ligand motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1975
Polymers22,9993
Non-polymers1982
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-4 kcal/mol
Surface area11340 Å2
Unit cell
Length a, b, c (Å)46.319, 58.710, 125.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HIV Tat-specific factor 1 / Tat-SF1


Mass: 11217.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTATSF1 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / References: UniProt: O43719
#2: Protein/peptide SF3b1 U2AF ligand motif


Mass: 563.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75533*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG 8000, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.099→37.314 Å / Num. obs: 37604 / % possible obs: 98.4 % / Redundancy: 5 % / Biso Wilson estimate: 33.59 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1650.6515910.9990.3610.75397
8.91-37.3144.90.03426810.0170.03888.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXdev_3051refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→37.314 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.2189 3675 9.77 %
Rwork0.1751 --
obs0.1794 37604 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.1 Å2 / Biso mean: 48.211 Å2 / Biso min: 20.87 Å2
Refinement stepCycle: final / Resolution: 2.099→37.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 31 151 1783
Biso mean--91.16 46.68 -
Num. residues----193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0994-2.1270.29721350.29591226136192
2.127-2.15610.31551370.25681282141998
2.1561-2.18690.28561500.24641355150597
2.1869-2.21960.26631410.21941304144598
2.2196-2.25420.28581450.2161313145897
2.2542-2.29120.24261410.22861297143897
2.2912-2.33070.26311470.21431331147898
2.3307-2.37310.24461350.19321272140797
2.3731-2.41870.25071380.19371318145698
2.4187-2.46810.23531430.20191295143896
2.4681-2.52170.27491430.20951273141695
2.5217-2.58040.28651440.20441339148398
2.5804-2.64490.24731430.20931290143398
2.6449-2.71640.22761400.19361334147498
2.7164-2.79630.25061470.19741333148098
2.7963-2.88650.2611420.18961321146398
2.8865-2.98960.20881370.19231312144998
2.9896-3.10930.22721390.18951302144196
3.1093-3.25070.23121380.17851280141895
3.2507-3.4220.1961390.17421310144998
3.422-3.63620.23271440.14931324146898
3.6362-3.91670.18591420.14971326146898
3.9167-4.31030.17881380.1331299143798
4.3103-4.93280.14771450.12761303144896
4.9328-6.21020.2041360.14891336147299
6.2102-37.31960.19941460.17511254140094
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)
11.08310.30760.70041.4454-0.40120.7176-0.19240.0712-0.1619-0.3864-0.3594-0.30230.80870.3393-00.40590.05520.08580.34580.07030.3437.3734-8.7121-40.6408
20.9842-0.1291-0.15820.6152-0.05541.43990.1699-0.7864-0.67771.4837-0.19710.659-0.55080.1167-0.02050.6951-0.02030.20550.36710.00450.5134-2.7114-16.2521-21.411
30.7891-0.19260.86720.6808-0.78541.47020.3273-0.3719-0.18590.79950.02970.9097-0.2998-0.24460.00110.58330.01870.25950.40660.05370.639-7.4634-6.4734-24.9648
41.269-0.1334-0.68560.3924-0.03990.40150.39020.23720.26880.5041-0.08060.9389-0.47-0.04350.00780.3521-0.00470.03440.32240.02590.3904-3.244-5.6252-36.1074
50.5211-0.3715-0.51041.7538-0.82363.66380.08150.10330.0920.169-0.12910.2919-0.08460.25900.322-0.00190.04160.2590.010.28193.1969-6.7254-34.1832
63.53711.3984-1.20292.9358-1.93381.30030.453-0.5948-0.11250.388-0.6938-0.3476-0.0821-0.00360.00030.5925-0.10970.03030.41630.04210.35776.3804-12.0271-29.251
70.28550.4346-1.05662.1072-0.9734.1886-0.292-0.15860.68650.4328-0.35621.18450.2747-2.35620.01640.28150.04690.03360.5796-0.17020.410210.0895-2.329316.2277
81.2148-0.87080.30850.8173-0.090.4243-0.21290.0755-0.2346-0.1881-0.01270.2001-0.1055-0.1927-0.00030.1952-0.01120.01020.4116-0.00190.34675.186-12.7679-4.8063
93.9526-1.3783-0.47431.6507-1.12432.31-0.13180.8124-0.4668-0.20260.3799-0.0426-0.09120.12720.00030.2491-0.02030.02720.4204-0.05660.287815.4296-13.5074-7.5969
100.79240.28360.20242.19111.09621.1197-0.28350.09170.0521-0.57670.2455-0.0748-0.1830.3052-0.01210.23430.0328-0.00650.3229-0.05460.288516.6693-8.88154.2653
111.0232-0.383-0.41210.566-0.14531.387-0.04490.3099-0.21410.07560.2174-0.00260.0066-0.000400.2110.0023-0.01240.2821-0.01840.23568.6151-12.14142.5606
120.52220.23840.32920.31850.31620.3375-0.27330.29930.1753-0.52890.08280.106-0.87950.3727-00.39490.0218-0.09010.29960.00650.29912.5072.10994.3855
132.67871.98031.41042.24991.76011.3985-0.83240.73520.7067-0.94310.69570.0791-1.05120.6665-0.00920.604-0.0163-0.12590.41050.07760.48945.5981-3.2403-9.011
140.77520.45620.00870.49650.30430.39020.0486-0.4520.1295-0.0081-0.22230.4140.0678-0.621400.30640.0401-0.03790.4867-0.04820.36473.2215-9.39177.7602
158.5065-7.3502-1.56826.35111.35490.28930.21730.22322.0511-0.1174-0.8743-1.0238-0.21871.40920.50671.3698-0.3186-0.14781.07380.08060.683812.8532-4.8109-11.8883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 259 through 269 )A259 - 269
2X-RAY DIFFRACTION2chain 'A' and (resid 270 through 277 )A270 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 297 )A278 - 297
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 307 )A298 - 307
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 332 )A308 - 332
6X-RAY DIFFRACTION6chain 'A' and (resid 333 through 353 )A333 - 353
7X-RAY DIFFRACTION7chain 'C' and (resid 260 through 264 )C260 - 264
8X-RAY DIFFRACTION8chain 'C' and (resid 265 through 277 )C265 - 277
9X-RAY DIFFRACTION9chain 'C' and (resid 278 through 297 )C278 - 297
10X-RAY DIFFRACTION10chain 'C' and (resid 298 through 306 )C298 - 306
11X-RAY DIFFRACTION11chain 'C' and (resid 307 through 321 )C307 - 321
12X-RAY DIFFRACTION12chain 'C' and (resid 322 through 332 )C322 - 332
13X-RAY DIFFRACTION13chain 'C' and (resid 333 through 342 )C333 - 342
14X-RAY DIFFRACTION14chain 'C' and (resid 343 through 353 )C343 - 353
15X-RAY DIFFRACTION15chain 'D' and (resid 336 through 339 )D336 - 339

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