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- PDB-7c08: Crystal structure of S34Y mutant of yeast U2AF1 complex bound to ... -

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Basic information

Entry
Database: PDB / ID: 7c08
TitleCrystal structure of S34Y mutant of yeast U2AF1 complex bound to 3' splice site RNA, 5'-UAGGU.
Components
  • RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
  • Splicing factor U2AF 23 kDa subunit
  • Splicing factor U2AF 59 kDa subunit
KeywordsSPLICING/RNA / pre-mRNA / splicing / intron / 3' splice site / zinc-finger / SPLICING-RNA complex
Function / homology
Function and homology information


mRNA branch site recognition / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex ...mRNA branch site recognition / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RNA recognition motif / RNA recognition motif ...U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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
RNA / Splicing factor U2AF 59 kDa subunit / Splicing factor U2AF 23 kDa subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsYoshida, H. / Park, S.Y. / Urano, T. / Obayashi, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06086 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.
Authors: Yoshida, H. / Park, S.Y. / Sakashita, G. / Nariai, Y. / Kuwasako, K. / Muto, Y. / Urano, T. / Obayashi, E.
History
DepositionApr 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Splicing factor U2AF 23 kDa subunit
B: Splicing factor U2AF 59 kDa subunit
C: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
D: Splicing factor U2AF 23 kDa subunit
E: Splicing factor U2AF 59 kDa subunit
F: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
G: Splicing factor U2AF 23 kDa subunit
H: Splicing factor U2AF 59 kDa subunit
I: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
J: Splicing factor U2AF 23 kDa subunit
K: Splicing factor U2AF 59 kDa subunit
L: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
M: Splicing factor U2AF 23 kDa subunit
N: Splicing factor U2AF 59 kDa subunit
O: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
P: Splicing factor U2AF 23 kDa subunit
Q: Splicing factor U2AF 59 kDa subunit
R: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
S: Splicing factor U2AF 23 kDa subunit
T: Splicing factor U2AF 59 kDa subunit
U: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
V: Splicing factor U2AF 23 kDa subunit
W: Splicing factor U2AF 59 kDa subunit
X: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
Y: Splicing factor U2AF 23 kDa subunit
Z: Splicing factor U2AF 59 kDa subunit
1: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,95745
Polymers313,77927
Non-polymers1,17718
Water0
1
A: Splicing factor U2AF 23 kDa subunit
B: Splicing factor U2AF 59 kDa subunit
C: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-45 kcal/mol
Surface area15750 Å2
MethodPISA
2
D: Splicing factor U2AF 23 kDa subunit
E: Splicing factor U2AF 59 kDa subunit
F: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-39 kcal/mol
Surface area14630 Å2
MethodPISA
3
G: Splicing factor U2AF 23 kDa subunit
H: Splicing factor U2AF 59 kDa subunit
I: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-41 kcal/mol
Surface area15720 Å2
MethodPISA
4
J: Splicing factor U2AF 23 kDa subunit
K: Splicing factor U2AF 59 kDa subunit
L: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-42 kcal/mol
Surface area15790 Å2
MethodPISA
5
M: Splicing factor U2AF 23 kDa subunit
N: Splicing factor U2AF 59 kDa subunit
O: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-41 kcal/mol
Surface area14490 Å2
MethodPISA
6
P: Splicing factor U2AF 23 kDa subunit
Q: Splicing factor U2AF 59 kDa subunit
R: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-41 kcal/mol
Surface area15650 Å2
MethodPISA
7
S: Splicing factor U2AF 23 kDa subunit
T: Splicing factor U2AF 59 kDa subunit
U: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-44 kcal/mol
Surface area14910 Å2
MethodPISA
8
V: Splicing factor U2AF 23 kDa subunit
W: Splicing factor U2AF 59 kDa subunit
X: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-38 kcal/mol
Surface area14640 Å2
MethodPISA
9
Y: Splicing factor U2AF 23 kDa subunit
Z: Splicing factor U2AF 59 kDa subunit
1: RNA (5'-R(*U*UP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9955
Polymers34,8643
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-71 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.506, 259.000, 94.822
Angle α, β, γ (deg.)90.000, 100.681, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
12
22
32
42
52
62
72
82
92
13
23
33
43
53
63
73
83
93

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111UUUUchain '1'1AA1 - 52 - 6
221UUUUchain 'C'CC1 - 52 - 6
331UUUUchain 'F'FF1 - 52 - 6
441UUUUchain 'I'II1 - 52 - 6
551UUUUchain 'L'LL1 - 52 - 6
661UUUUchain 'O'OO1 - 52 - 6
771UUUUchain 'R'RR1 - 52 - 6
881UUUUchain 'U'UU1 - 52 - 6
991UUUUchain 'X'XX1 - 52 - 6
1102VALVALILEILE(chain 'A' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))AA16 - 5616 - 56
1112GLYGLYGLYGLY(chain 'A' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))AA61 - 10061 - 100
1122LEULEUALAALA(chain 'A' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))AA103 - 191103 - 191
2132VALVALILEILE(chain 'D' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))DD16 - 5616 - 56
2142GLYGLYGLYGLY(chain 'D' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))DD61 - 10061 - 100
2152LEULEUALAALA(chain 'D' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))DD103 - 191103 - 191
3162VALVALILEILE(chain 'G' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))GG16 - 5616 - 56
3172GLYGLYGLYGLY(chain 'G' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))GG61 - 10061 - 100
3182LEULEUALAALA(chain 'G' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))GG103 - 191103 - 191
4192VALVALILEILE(chain 'J' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))JJ16 - 5616 - 56
4202GLYGLYGLYGLY(chain 'J' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))JJ61 - 10061 - 100
4212LEULEUALAALA(chain 'J' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))JJ103 - 191103 - 191
5222VALVALILEILE(chain 'M' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))MM16 - 5616 - 56
5232GLYGLYGLYGLY(chain 'M' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))MM61 - 10061 - 100
5242LEULEUALAALA(chain 'M' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))MM103 - 191103 - 191
6252VALVALILEILE(chain 'P' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))PP16 - 5616 - 56
6262GLYGLYGLYGLY(chain 'P' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))PP61 - 10061 - 100
6272LEULEUALAALA(chain 'P' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))PP103 - 191103 - 191
7282VALVALILEILE(chain 'S' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))SS16 - 5616 - 56
7292GLYGLYGLYGLY(chain 'S' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))SS61 - 10061 - 100
7302LEULEUALAALA(chain 'S' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))SS103 - 191103 - 191
8312VALVALILEILE(chain 'V' and (resid 16 through 101 or resid 103 through 192))VV16 - 5616 - 56
8322GLYGLYGLYGLY(chain 'V' and (resid 16 through 101 or resid 103 through 192))VV61 - 10061 - 100
8332LEULEUALAALA(chain 'V' and (resid 16 through 101 or resid 103 through 192))VV103 - 191103 - 191
9342VALVALILEILE(chain 'Y' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))YY16 - 5616 - 56
9352GLYGLYGLYGLY(chain 'Y' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))YY61 - 10061 - 100
9362LEULEUALAALA(chain 'Y' and (resid 16 through 57 or resid 61 through 101 or resid 103 through 192))YY103 - 191103 - 191
1373GLUGLUPROPRO(chain 'B' and resid 113 through 160)BB113 - 15921 - 67
2383GLUGLUPROPRO(chain 'E' and resid 113 through 160)EE113 - 15921 - 67
3393GLUGLUPROPRO(chain 'H' and resid 113 through 160)HH113 - 15921 - 67
4403GLUGLUPROPRO(chain 'K' and resid 113 through 160)KK113 - 15921 - 67
5413GLUGLUPROPRO(chain 'N' and resid 113 through 160)NN113 - 15921 - 67
6423GLUGLUPROPRO(chain 'Q' and resid 113 through 160)QQ113 - 15921 - 67
7433GLUGLUPROPRO(chain 'T' and resid 113 through 160)TT113 - 15921 - 67
8443GLUGLUPROPRO(chain 'W' and resid 113 through 160)WW113 - 15921 - 67
9453GLUGLUPROPROchain 'Z'ZZ113 - 15921 - 67

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Splicing factor U2AF 23 kDa subunit / U2 auxiliary factor 23 kDa subunit / U2AF23 / U2 snRNP auxiliary factor small subunit


Mass: 25142.344 Da / Num. of mol.: 9 / Mutation: S34Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: SPAP8A3.06 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09176
#2: Protein
Splicing factor U2AF 59 kDa subunit / U2 auxiliary factor 59 kDa subunit / U2AF59 / U2 snRNP auxiliary factor large subunit


Mass: 7828.880 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: prp2, mis11, SPBC146.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P36629
#3: RNA chain
RNA (5'-R(*U*UP*AP*GP*GP*U)-3')


Mass: 1893.157 Da / Num. of mol.: 9 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.63 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaCitrate, 10% PEG 35000 / PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.35→48.4 Å / Num. obs: 64167 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 65.38 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.23 / Net I/σ(I): 8.3
Reflection shellResolution: 3.35→3.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4510 / CC1/2: 0.742 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YH8

4yh8


Resolution: 3.35→46.59 Å / SU ML: 0.4894 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6957
RfactorNum. reflection% reflection
Rfree0.2523 3248 5.07 %
Rwork0.2143 --
obs0.2162 64058 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.69 Å2
Refinement stepCycle: LAST / Resolution: 3.35→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17476 945 18 0 18439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001818963
X-RAY DIFFRACTIONf_angle_d0.500125808
X-RAY DIFFRACTIONf_chiral_restr0.03882690
X-RAY DIFFRACTIONf_plane_restr0.0043248
X-RAY DIFFRACTIONf_dihedral_angle_d16.91542886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40.39751490.31332633X-RAY DIFFRACTION100
3.4-3.450.35371410.3032656X-RAY DIFFRACTION99.79
3.45-3.510.33761250.2942641X-RAY DIFFRACTION99.86
3.51-3.570.33771490.28212586X-RAY DIFFRACTION99.89
3.57-3.640.3341360.27232707X-RAY DIFFRACTION99.93
3.64-3.710.29151500.26012569X-RAY DIFFRACTION99.96
3.71-3.780.28931650.24972689X-RAY DIFFRACTION99.93
3.78-3.860.29471310.24732597X-RAY DIFFRACTION99.89
3.86-3.950.32831440.24852669X-RAY DIFFRACTION99.89
3.95-4.050.27521500.23852624X-RAY DIFFRACTION100
4.05-4.160.28661660.2272621X-RAY DIFFRACTION99.82
4.16-4.280.21631590.20992619X-RAY DIFFRACTION100
4.28-4.420.2481300.19832613X-RAY DIFFRACTION100
4.42-4.580.24351560.18592643X-RAY DIFFRACTION99.93
4.58-4.760.23311190.19472674X-RAY DIFFRACTION100
4.76-4.980.23061120.18362689X-RAY DIFFRACTION99.93
4.98-5.240.27871080.19522669X-RAY DIFFRACTION99.96
5.24-5.570.22391700.19442616X-RAY DIFFRACTION99.75
5.57-60.23161590.18512618X-RAY DIFFRACTION99.86
6-6.60.24071220.19632666X-RAY DIFFRACTION100
6.6-7.550.25011280.192672X-RAY DIFFRACTION99.93
7.55-9.50.16111390.16812683X-RAY DIFFRACTION100
9.5-46.590.15871400.17252656X-RAY DIFFRACTION99.01

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