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- PDB-6n3d: Structure of HIV Tat-specific factor 1 U2AF Homology Motif (APO-State) -

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Basic information

Entry
Database: PDB / ID: 6n3d
TitleStructure of HIV Tat-specific factor 1 U2AF Homology Motif (APO-State)
ComponentsHIV Tat-specific factor 1
KeywordsPEPTIDE BINDING PROTEIN / HIV Tat-specific factor 1 / TAT-SF1 / RNA SPLICING FACTOR / U2AF HOMOLOGY MOTIF / UHM / RNA BINDING PROTEIN / U2AF LIGAND MOTIF / ULM / PRE-MRNA SPLICING FACTOR
Function / homology
Function and homology information


poly-ADP-D-ribose modification-dependent protein binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / mRNA Splicing - Major Pathway / spliceosomal complex / double-strand break repair via homologous recombination / mRNA splicing, via spliceosome ...poly-ADP-D-ribose modification-dependent protein binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / mRNA Splicing - Major Pathway / spliceosomal complex / double-strand break repair via homologous recombination / 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
DI(HYDROXYETHYL)ETHER / 17S U2 SnRNP complex component HTATSF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5828
Polymers11,2181
Non-polymers3647
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-30 kcal/mol
Surface area5760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.201, 30.201, 98.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#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 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / References: UniProt: O43719

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Non-polymers , 5 types, 119 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 8000, 0.4 M MgCl2, 0.1 M TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8265 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 1.13→30.2 Å / Num. obs: 61046 / % possible obs: 98.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 11.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Net I/σ(I): 13.6
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1696 / CC1/2: 0.84 / Rpim(I) all: 0.252 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.1.26data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXW, 2PEH, 4OZ0

4fxw

2peh

4oz0


Resolution: 1.13→30.2 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.57
RfactorNum. reflection% reflection
Rfree0.1596 2324 3.81 %
Rwork0.1273 --
obs0.1285 61046 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.44 Å2 / Biso mean: 20.5131 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 1.13→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 36 114 930
Biso mean--47.62 36.37 -
Num. residues----96
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.13-1.15310.2411380.21023466360492
1.1531-1.17820.23081260.20383395352192
1.1782-1.20560.24571530.19553456360992
1.2056-1.23570.20371230.17813329345292
1.2357-1.26910.17581360.1733336347290
1.2691-1.30650.18321370.15253458359594
1.3065-1.34870.21121330.14233461359494
1.3487-1.39690.18231330.13093468360194
1.3969-1.45280.171350.12543494362994
1.4528-1.51890.15051360.11523468360494
1.5189-1.5990.14711390.10843444358393
1.599-1.69910.12211300.09883518364895
1.6991-1.83030.12231430.10463480362395
1.8303-2.01450.13121480.1053503365194
2.0145-2.30590.12291370.10373406354393
2.3059-2.90480.17471430.12823559370296
2.9048-30.21180.16661340.13363481361594

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