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- PDB-7q8a: Crystal structure of tandem domain RRM1-2 of FUBP-interacting rep... -

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Basic information

Entry
Database: PDB / ID: 7q8a
TitleCrystal structure of tandem domain RRM1-2 of FUBP-interacting repressor (FIR) bound to FUSE ssDNA fragment
Components
  • DNA (5'-D(P*GP*T)-3')
  • Poly(U)-binding-splicing factor PUF60
  • ssDNA
KeywordsTRANSCRIPTION / RNA recognition motif(RRM) / ssDNA / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mRNA splice site recognition / alternative mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding ...mRNA splice site recognition / alternative mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...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 / 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
Similarity search - Domain/homology
DNA / Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNi, X. / Joerger, A.C. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of tandem domain RRM1-2 of FIR bound to FUSE ssDNA fragment
Authors: Ni, X. / Joerger, A.C. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionNov 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 2.0Jan 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref_seq
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Description: Ligand identity / Details: modify bound nucleotide / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(U)-binding-splicing factor PUF60
B: Poly(U)-binding-splicing factor PUF60
D: DNA (5'-D(P*GP*T)-3')
E: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4938
Polymers45,2444
Non-polymers2484
Water2,288127
1
A: Poly(U)-binding-splicing factor PUF60
E: ssDNA


Theoretical massNumber of molelcules
Total (without water)22,6102
Polymers22,6102
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(U)-binding-splicing factor PUF60
D: DNA (5'-D(P*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8836
Polymers22,6352
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.696, 69.785, 107.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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: 22046.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUF60, FIR, ROBPI, SIAHBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UHX1
#2: DNA chain DNA (5'-D(P*GP*T)-3')


Mass: 588.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain ssDNA


Mass: 563.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 25% w/v PEG3350, 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris , pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.05→42.5 Å / Num. obs: 26557 / % possible obs: 98.9 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 1979 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFJ

2qfj


Resolution: 2.05→42.5 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 2345 4.74 %
Rwork0.1986 --
obs0.2008 26557 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 82 16 127 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.886
X-RAY DIFFRACTIONf_dihedral_angle_d10.514468
X-RAY DIFFRACTIONf_chiral_restr0.056464
X-RAY DIFFRACTIONf_plane_restr0.01547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.32421270.27442683X-RAY DIFFRACTION96
2.09-2.140.31981280.25722556X-RAY DIFFRACTION90
2.14-2.190.32921780.24392752X-RAY DIFFRACTION98
2.19-2.240.23011510.23122793X-RAY DIFFRACTION99
2.24-2.30.34311500.2232765X-RAY DIFFRACTION99
2.3-2.370.31071160.22192822X-RAY DIFFRACTION99
2.37-2.450.2641440.21882818X-RAY DIFFRACTION98
2.45-2.530.25451290.21662814X-RAY DIFFRACTION99
2.53-2.640.26191290.21632799X-RAY DIFFRACTION99
2.64-2.760.25571290.22772794X-RAY DIFFRACTION99
2.76-2.90.28311530.21212761X-RAY DIFFRACTION98
2.9-3.080.25811370.21012683X-RAY DIFFRACTION94
3.08-3.320.32011320.21082819X-RAY DIFFRACTION100
3.32-3.650.21721290.19242827X-RAY DIFFRACTION100
3.65-4.180.20961470.16662820X-RAY DIFFRACTION100
4.18-5.270.21721360.15862801X-RAY DIFFRACTION98
5.27-42.50.19461300.19012780X-RAY DIFFRACTION98

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