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- PDB-7c07: Crystal structure of yeast U2AF1 complex bound to 5'-AAGGU RNA. -

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Basic information

Entry
Database: PDB / ID: 7c07
TitleCrystal structure of yeast U2AF1 complex bound to 5'-AAGGU RNA.
Components
  • RNA (5'-R(*U*AP*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: 3.2 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*AP*AP*GP*GP*U)-3')
D: Splicing factor U2AF 23 kDa subunit
E: Splicing factor U2AF 59 kDa subunit
F: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
G: Splicing factor U2AF 23 kDa subunit
H: Splicing factor U2AF 59 kDa subunit
I: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
J: Splicing factor U2AF 23 kDa subunit
K: Splicing factor U2AF 59 kDa subunit
L: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
M: Splicing factor U2AF 23 kDa subunit
N: Splicing factor U2AF 59 kDa subunit
O: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
P: Splicing factor U2AF 23 kDa subunit
Q: Splicing factor U2AF 59 kDa subunit
R: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
S: Splicing factor U2AF 23 kDa subunit
T: Splicing factor U2AF 59 kDa subunit
U: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
V: Splicing factor U2AF 23 kDa subunit
W: Splicing factor U2AF 59 kDa subunit
X: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
Y: Splicing factor U2AF 23 kDa subunit
Z: Splicing factor U2AF 59 kDa subunit
1: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,47945
Polymers313,30227
Non-polymers1,17718
Water0
1
A: Splicing factor U2AF 23 kDa subunit
B: Splicing factor U2AF 59 kDa subunit
C: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Splicing factor U2AF 23 kDa subunit
E: Splicing factor U2AF 59 kDa subunit
F: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Splicing factor U2AF 23 kDa subunit
H: Splicing factor U2AF 59 kDa subunit
I: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Splicing factor U2AF 23 kDa subunit
K: Splicing factor U2AF 59 kDa subunit
L: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Splicing factor U2AF 23 kDa subunit
N: Splicing factor U2AF 59 kDa subunit
O: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Splicing factor U2AF 23 kDa subunit
Q: Splicing factor U2AF 59 kDa subunit
R: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Splicing factor U2AF 23 kDa subunit
T: Splicing factor U2AF 59 kDa subunit
U: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: Splicing factor U2AF 23 kDa subunit
W: Splicing factor U2AF 59 kDa subunit
X: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Y: Splicing factor U2AF 23 kDa subunit
Z: Splicing factor U2AF 59 kDa subunit
1: RNA (5'-R(*U*AP*AP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9425
Polymers34,8113
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.487, 256.947, 94.591
Angle α, β, γ (deg.)90.000, 100.751, 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
14
24

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
111AAUUchain '1'1AA1 - 52 - 6
221AAUUchain 'C'CC1 - 52 - 6
331AAUUchain 'F'FF1 - 52 - 6
441AAUUchain 'I'II1 - 52 - 6
551AAUUchain 'L'LL1 - 52 - 6
661AAUUchain 'O'OO1 - 52 - 6
771AAUUchain 'R'RR1 - 52 - 6
881AAUUchain 'U'UU1 - 52 - 6
991AAUUchain 'X'XX1 - 52 - 6
1102VALVALILEILE(chain 'A' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))AA16 - 5616 - 56
1112LYSLYSGLYGLY(chain 'A' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))AA62 - 10062 - 100
1122LEULEUALAALA(chain 'A' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))AA103 - 191103 - 191
2132VALVALILEILE(chain 'D' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))DD16 - 5616 - 56
2142LYSLYSGLYGLY(chain 'D' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))DD62 - 10062 - 100
2152LEULEUALAALA(chain 'D' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))DD103 - 191103 - 191
3162VALVALILEILE(chain 'G' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))GG16 - 5616 - 56
3172LYSLYSGLYGLY(chain 'G' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))GG62 - 10062 - 100
3182LEULEUALAALA(chain 'G' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))GG103 - 191103 - 191
4192VALVALILEILE(chain 'J' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))JJ16 - 5616 - 56
4202LYSLYSGLYGLY(chain 'J' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))JJ62 - 10062 - 100
4212LEULEUALAALA(chain 'J' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))JJ103 - 191103 - 191
5222VALVALILEILE(chain 'M' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))MM16 - 5616 - 56
5232LYSLYSGLYGLY(chain 'M' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))MM62 - 10062 - 100
5242LEULEUALAALA(chain 'M' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))MM103 - 191103 - 191
6252VALVALILEILE(chain 'P' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))PP16 - 5616 - 56
6262LYSLYSGLYGLY(chain 'P' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))PP62 - 10062 - 100
6272LEULEUALAALA(chain 'P' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))PP103 - 191103 - 191
7282VALVALILEILE(chain 'S' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))SS16 - 5616 - 56
7292LYSLYSGLYGLY(chain 'S' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))SS62 - 10062 - 100
7302LEULEUALAALA(chain 'S' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))SS103 - 191103 - 191
8312VALVALILEILE(chain 'V' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))VV16 - 5616 - 56
8322LYSLYSGLYGLY(chain 'V' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))VV62 - 10062 - 100
8332LEULEUALAALA(chain 'V' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))VV103 - 191103 - 191
9342VALVALILEILE(chain 'Y' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))YY16 - 5616 - 56
9352LYSLYSGLYGLY(chain 'Y' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))YY62 - 10062 - 100
9362LEULEUALAALA(chain 'Y' and (resid 16 through 57 or resid 62 through 101 or resid 103 through 192))YY103 - 191103 - 191
1373ARGARGLEULEU(chain 'B' and resid 110 through 159)BB110 - 15818 - 66
2383ARGARGLEULEU(chain 'E' and resid 110 through 159)EE110 - 15818 - 66
3393ARGARGLEULEU(chain 'H' and resid 110 through 159)HH110 - 15818 - 66
4403ARGARGLEULEU(chain 'K' and resid 110 through 159)KK110 - 15818 - 66
5413ARGARGLEULEU(chain 'N' and resid 110 through 159)NN110 - 15818 - 66
6423ARGARGLEULEU(chain 'Q' and resid 110 through 159)QQ110 - 15818 - 66
7433ARGARGLEULEU(chain 'W' and resid 110 through 159)WW110 - 15818 - 66
1444GLUGLUARGARG(chain 'T' and (resid 115 through 120 or resid 123 through 160))TT115 - 12023 - 28
1454THRTHRPROPRO(chain 'T' and (resid 115 through 120 or resid 123 through 160))TT123 - 15931 - 67
2464GLUGLUARGARGchain 'Z'ZZ115 - 12023 - 28
2474THRTHRPROPROchain 'Z'ZZ123 - 15931 - 67

NCS ensembles :
ID
1
2
3
4

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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: 25066.248 Da / Num. of mol.: 9
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*AP*AP*GP*GP*U)-3')


Mass: 1916.197 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: 3.6 Å3/Da / Density % sol: 71.28 %
Crystal growTemperature: 277 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: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48.17 Å / Num. obs: 72802 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 73.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.2
Reflection shellResolution: 3.2→3.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4522 / CC1/2: 0.638 / % 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: 3.2→48.17 Å / SU ML: 0.5254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8574
RfactorNum. reflection% reflection
Rfree0.2854 3655 5.02 %
Rwork0.2547 --
obs0.2563 72746 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.44 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17399 963 18 0 18380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001618901
X-RAY DIFFRACTIONf_angle_d0.447125722
X-RAY DIFFRACTIONf_chiral_restr0.03832685
X-RAY DIFFRACTIONf_plane_restr0.00283232
X-RAY DIFFRACTIONf_dihedral_angle_d17.44922871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.40841370.34892698X-RAY DIFFRACTION99.96
3.24-3.290.40651360.34812626X-RAY DIFFRACTION99.96
3.29-3.330.39461180.33612655X-RAY DIFFRACTION100
3.33-3.380.3671540.31122697X-RAY DIFFRACTION99.93
3.38-3.440.32621180.30592607X-RAY DIFFRACTION100
3.44-3.490.32771360.30482697X-RAY DIFFRACTION100
3.49-3.550.34021330.29382630X-RAY DIFFRACTION100
3.55-3.620.3711500.29772661X-RAY DIFFRACTION100
3.62-3.690.32341340.29712624X-RAY DIFFRACTION99.96
3.69-3.760.361280.28522698X-RAY DIFFRACTION100
3.76-3.840.29321400.29352652X-RAY DIFFRACTION100
3.84-3.930.33951420.28282668X-RAY DIFFRACTION100
3.93-4.030.28661370.28132628X-RAY DIFFRACTION100
4.03-4.140.28741410.26552682X-RAY DIFFRACTION100
4.14-4.260.28851490.24642609X-RAY DIFFRACTION100
4.26-4.40.26351560.2522607X-RAY DIFFRACTION100
4.4-4.560.32371490.24782701X-RAY DIFFRACTION100
4.56-4.740.27161370.24442659X-RAY DIFFRACTION100
4.74-4.950.28061510.23172641X-RAY DIFFRACTION100
4.95-5.220.24341190.23692673X-RAY DIFFRACTION99.96
5.22-5.540.24981280.23732682X-RAY DIFFRACTION99.79
5.54-5.970.26581550.22982645X-RAY DIFFRACTION99.93
5.97-6.570.29971560.23722619X-RAY DIFFRACTION100
6.57-7.510.22931430.22612685X-RAY DIFFRACTION99.93
7.52-9.450.21651590.2022682X-RAY DIFFRACTION100
9.46-48.170.21061490.19772665X-RAY DIFFRACTION99.5

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