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- PDB-6n3e: Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound ... -

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Basic information

Entry
Database: PDB / ID: 6n3e
TitleStructure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4
Components
  • HIV Tat-specific factor 1
  • SF3b1 U2AF ligand motif
KeywordsPROTEIN BINDING / HIV Tat-specific factor 1 / RNA SPLICING FACTOR / U2AF HOMOLOGY MOTIF / UHM / RNA BINDING PROTEIN / U2AF LIGAND MOTIF / ULM / PROTEIN-PEPTIDE COMPLEX / PRE-MRNA SPLICING FACTOR
Function / homology
Function and homology information


U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / poly-ADP-D-ribose modification-dependent protein binding / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome ...U11/U12 snRNP / chromatin-protein adaptor activity / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / protein localization to site of double-strand break / 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 / spliceosomal complex / double-strand break repair via homologous recombination / 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
FORMIC ACID / 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: 1.893 Å
AuthorsLoerch, S. / 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
B: SF3b1 U2AF ligand motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2744
Polymers12,1362
Non-polymers1382
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 58.370, 97.310
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-510-

HOH

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Components

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


Mass: 11217.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTATSF1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43719
#2: Protein/peptide SF3b1 U2AF ligand motif


Mass: 917.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75533*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate dihydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.89→35.055 Å / Num. obs: 15748 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 29.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.049 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.89-1.943.90.4529200.8120.2430.51892.1
9.08-35.0554.70.0251820.9980.0130.02898.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.1.26data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.893→35.055 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.1983 1451 9.21 %
Rwork0.1714 --
obs0.1739 15748 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.77 Å2 / Biso mean: 48.9448 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 1.893→35.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 18 105 960
Biso mean--70.22 51.38 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01903
X-RAY DIFFRACTIONf_angle_d0.9711226
X-RAY DIFFRACTIONf_chiral_restr0.066123
X-RAY DIFFRACTIONf_plane_restr0.007168
X-RAY DIFFRACTIONf_dihedral_angle_d15.095538
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.893-1.96060.29141340.2506132894
1.9606-2.03910.23951480.19451409100
2.0391-2.13190.21591400.18261411100
2.1319-2.24430.19331450.16791424100
2.2443-2.38490.18871410.16341414100
2.3849-2.5690.17081450.17151436100
2.569-2.82740.22181490.18021424100
2.8274-3.23630.22351480.17541454100
3.2363-4.07640.17091470.14891450100
4.0764-35.0550.19461540.17361547100
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)
11.0660.28850.74871.08150.90381.3340.059-0.26850.32710.1876-0.31040.1574-0.309-0.09690.16360.3969-0.1714-0.01110.3094-0.02440.310915.0785-14.5395-1.6673
21.57641.37341.12661.94430.97322.6059-0.0293-0.6660.09690.7493-0.0116-0.02430.23540.06290.05370.9941-0.4234-0.03690.79710.03490.418314.8031-18.996113.9098
32.18170.51940.63451.89271.83751.80760.0585-0.12280.16650.3338-0.2921-0.0388-0.44020.04720.28330.4672-0.194-0.08590.23740.06440.32420.4938-11.8280.2914
42.79051.57150.61394.35182.09551.02440.3632-0.345-0.06260.6973-0.0737-0.69370.28690.0038-0.09770.6806-0.3233-0.24040.27810.1310.49824.9511-21.41447.5195
51.39311.4170.28872.40150.8090.51160.04650.0916-0.12310.16680.0027-0.25250.0930.0938-0.03450.4333-0.156-0.09310.24690.03150.333523.7202-15.3778-0.9954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 314 through 353 )A314 - 353
2X-RAY DIFFRACTION2chain 'B' and (resid 291 through 297 )B291 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 277 )A260 - 277
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 297 )A278 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 313 )A298 - 313

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