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- PDB-7z3x: Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA -

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Basic information

Entry
Database: PDB / ID: 7z3x
TitleCrystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA
Components
  • DNA (5'-D(*TP*TP*T)-3')
  • DNA (5'-D(P*GP*TP*())-3')
  • Poly(U)-binding-splicing factor PUF60
KeywordsDNA BINDING PROTEIN / RNA recognition motif (RRM) / ssDNA
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / 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. / RNA recognition motif domain ...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: 1.65 Å
AuthorsNi, X. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA
Authors: Ni, X. / Chaikuad, A. / Knapp, S.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 2.0Jan 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_contact_author / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity.pdbx_description / _entity.pdbx_number_of_molecules ..._entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _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_atom_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_atom_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_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_work / _refine.pdbx_overall_phase_error / _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_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sheet_id
Description: Model completeness / 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*TP*())-3')
E: DNA (5'-D(*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6168
Polymers45,3684
Non-polymers2484
Water3,189177
1
A: Poly(U)-binding-splicing factor PUF60
D: DNA (5'-D(P*GP*TP*())-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8214
Polymers22,6972
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(U)-binding-splicing factor PUF60
E: DNA (5'-D(*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7964
Polymers22,6722
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.613, 70.386, 107.353
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: 21803.891 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*TP*())-3')


Mass: 892.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*TP*T)-3')


Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350 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: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.65→49.38 Å / Num. obs: 50994 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 2538 / CC1/2: 0.833

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Processing

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

2qfj


Resolution: 1.65→49.38 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 2554 5.01 %
Rwork0.2038 --
obs0.2044 50947 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 87 16 177 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.041
X-RAY DIFFRACTIONf_dihedral_angle_d9.207476
X-RAY DIFFRACTIONf_chiral_restr0.059466
X-RAY DIFFRACTIONf_plane_restr0.008546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.38711340.33652683X-RAY DIFFRACTION100
1.68-1.720.35451490.30042653X-RAY DIFFRACTION100
1.72-1.750.30661450.26752683X-RAY DIFFRACTION100
1.75-1.790.30511350.2472684X-RAY DIFFRACTION100
1.79-1.840.24931560.23062606X-RAY DIFFRACTION99
1.84-1.890.24661190.22422663X-RAY DIFFRACTION98
1.89-1.940.26661540.22842670X-RAY DIFFRACTION100
1.94-2.010.26191610.24182658X-RAY DIFFRACTION100
2.01-2.080.27291440.23122695X-RAY DIFFRACTION100
2.08-2.160.20911400.20712664X-RAY DIFFRACTION100
2.16-2.260.22271350.1972703X-RAY DIFFRACTION100
2.26-2.380.2441320.20812717X-RAY DIFFRACTION100
2.38-2.530.2491350.21242711X-RAY DIFFRACTION99
2.53-2.720.24451410.2132606X-RAY DIFFRACTION96
2.72-30.23211180.20852748X-RAY DIFFRACTION99
3-3.430.22481540.20752725X-RAY DIFFRACTION99
3.43-4.320.17111530.16862748X-RAY DIFFRACTION99
4.32-49.380.15631490.18632776X-RAY DIFFRACTION95
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)
15.54781.9078-3.60846.3879-3.48528.68-0.05160.02520.3395-0.53420.1128-0.3758-0.12460.3285-0.08980.3144-0.0447-0.0060.1563-0.00390.271-2.97575.48119.7561
21.93540.31811.11583.17250.3612.8696-0.0274-0.46880.24810.38010.05710.1355-0.3794-0.6445-0.07830.28620.08540.01950.3009-0.03010.208-11.8553-1.132142.8833
35.51820.3283-2.10612.4399-1.78316.3192-0.0913-0.10350.17390.00850.0379-0.0969-0.1623-0.13790.08720.1790.0287-0.01010.1683-0.00610.1497-7.0484-6.006732.0902
41.72790.8073-0.61383.5099-3.07029.2942-0.0684-0.19110.04470.2750.19840.1942-0.161-0.9031-0.16190.16550.02170.01090.24120.00450.189-15.7938-5.23132.8674
59.3021-6.3032-0.4188.2619-0.06196.08550.54130.8422-0.0231-1.1809-0.33010.16050.12450.2089-0.15950.31380.001-0.00980.20620.00520.1513-5.0943-5.915414.3087
63.2737-0.5925-0.84365.6683-0.34295.03340.0171-0.02190.18520.0001-0.1261-0.5640.04970.57910.06490.13380.0465-0.00270.17980.02280.2236.8703-15.436229.0899
74.3775-1.65571.58956.4274-0.93483.5269-0.09920.40230.25920.06340.0716-0.5621-0.28570.15820.26710.19210.01090.02250.1866-0.00040.21870.3825-9.624523.0557
85.5136-0.0768-0.27030.69780.89691.17040.10260.221-0.413-0.10860.36490.91110.0359-0.8641-0.22070.321-0.0351-0.09720.62970.27940.5666-37.2317-1.18228.2369
91.8587-1.13510.97864.7184-3.52775.0305-0.0037-0.1361-0.06620.01260.23690.2736-0.1268-0.2298-0.15740.19490.0111-0.01050.17780.01370.185-21.37354.77947.1351
100.26341.1062-0.19864.8436-1.17173.46530.0711-0.432-0.07740.2126-0.04190.9283-0.4996-0.0535-0.07020.30810.02480.09850.62570.20320.7326-40.6816-4.396919.0608
114.3503-0.0179-0.7753.0478-1.13771.1127-0.535-1.1073-1.28550.07810.65620.3310.4453-0.18270.05380.31010.06660.02260.54150.27640.505-22.6283-15.756719.2307
122.79130.0796-1.92853.0363-2.64323.57410.70620.00620.6044-0.2494-0.16891.114-1.0123-1.8271-0.39970.54060.1832-0.00470.74850.06590.4526-22.37911.553135.6201
136.77384.3704-2.84857.41711.35196.2956-0.51260.65380.697-1.03150.8931.3542-0.3984-0.8975-0.47660.50830.1268-0.07440.6470.19680.6032-30.893811.86995.2408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 196 )
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 291 )
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 117 )
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 191 )
10X-RAY DIFFRACTION10chain 'B' and (resid 192 through 208 )
11X-RAY DIFFRACTION11chain 'B' and (resid 209 through 289 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 3 )
13X-RAY DIFFRACTION13chain 'E' and (resid 0 through 2 )

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