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- PDB-6nsx: Yeast Hsh155 Ligand bound to Human Tat-SF1 Motif -

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Basic information

Entry
Database: PDB / ID: 6nsx
TitleYeast Hsh155 Ligand bound to Human Tat-SF1 Motif
Components
  • HIV Tat-specific factor 1
  • Hsh155
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 / HSH155 / SF3B1
Function / homology
Function and homology information


chromatin-protein adaptor activity / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / mRNA Splicing - Major Pathway / double-strand break repair via homologous recombination / spliceosomal complex / mRNA splicing, via spliceosome ...chromatin-protein adaptor activity / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / mRNA Splicing - Major Pathway / double-strand break repair via homologous recombination / spliceosomal complex / mRNA splicing, via spliceosome / site of double-strand break / RNA binding / nucleoplasm / nucleus
Similarity search - Function
TatSF1-like, RNA recognition motif 1 / TatSF1-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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...TatSF1-like, RNA recognition motif 1 / TatSF1-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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
17S U2 SnRNP complex component HTATSF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsJenkins, J.L. / Leach, J.R. / 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: Rna / Year: 2019
Title: Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction.
Authors: Talkish, J. / Igel, H. / Hunter, O. / Horner, S.W. / Jeffery, N.N. / Leach, J.R. / Jenkins, J.L. / Kielkopf, C.L. / Ares, M.
History
DepositionJan 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
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
B: Hsh155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9364
Polymers11,8652
Non-polymers712
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-15 kcal/mol
Surface area5950 Å2
Unit cell
Length a, b, c (Å)58.581, 58.581, 97.572
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

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


Mass: 11073.468 Da / Num. of mol.: 1
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 Hsh155


Mass: 791.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→35.165 Å / Num. obs: 13598 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.034 / Rrim(I) all: 0.102 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.058.91.0239590.9020.3591.08698.7
8.94-35.167.70.0791910.9960.030.08598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N3E

6n3e


Resolution: 2→35.165 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 21.3
RfactorNum. reflection% reflection
Rfree0.1942 2305 9.12 %
Rwork0.1768 --
obs0.1785 25286 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.43 Å2 / Biso mean: 66.0279 Å2 / Biso min: 33.37 Å2
Refinement stepCycle: final / Resolution: 2→35.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 2 66 897
Biso mean--85.13 56.93 -
Num. residues----100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.04380.32531480.2911413156199
2.0438-2.09130.29321470.252914621609100
2.0913-2.14360.25351380.239714091547100
2.1436-2.20150.26211470.22114431590100
2.2015-2.26630.26081410.221214621603100
2.2663-2.33950.27271480.218314071555100
2.3395-2.4230.20991420.194114851627100
2.423-2.520.21721440.201613991543100
2.52-2.63470.21361430.201514121555100
2.6347-2.77350.19311360.214814881624100
2.7735-2.94720.2381380.200714211559100
2.9472-3.17470.22781390.197414371576100
3.1747-3.49390.18611480.172514321580100
3.4939-3.99880.15631420.155614371579100
3.9988-5.03580.14821530.126714321585100
5.0358-35.17040.18751510.167514421593100
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)
13.0651-1.6526-2.88455.00953.66654.1777-0.1854-0.43050.41290.46510.2431-0.114-0.2387-0.2240.06870.62340.2304-0.05730.3362-0.00720.437622.358613.5403-13.6116
22.5127-1.4396-0.39478.72575.57034.8871-0.4979-0.39430.19321.0320.9672-0.53210.39680.8576-0.31430.7820.3453-0.12130.5898-0.07010.507731.02997.7319-11.306
32.4901-2.735-0.89634.29161.90841.8272-0.252-0.23320.2438-0.02550.3875-0.3186-0.06820.2728-0.150.66280.2351-0.04830.3989-0.060.423425.300112.9202-17.2464
42.2407-0.4011-1.31144.30842.95772.7405-0.263-0.14650.09210.4440.02360.31460.095-0.33350.23570.67620.18840.00080.33540.01790.370420.25095.931-17.848
54.64033.5635-2.94992.82-2.34731.93490.39370.24290.12570.4460.3646-0.6285-0.4043-0.327-0.5812.08310.50460.03610.9914-0.05740.878224.91923.8454-3.1095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 282 )A260 - 282
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 297 )A283 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 313 )A298 - 313
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 353 )A314 - 353
5X-RAY DIFFRACTION5chain 'B' and (resid 99 through 104 )B99 - 104

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