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- PDB-7c06: Crystal structure of yeast U2AF1 complex bound to 3' splice site ... -

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Basic information

Entry
Database: PDB / ID: 7c06
TitleCrystal structure 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


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / commitment complex / mRNA cis splicing, via spliceosome / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / commitment complex / mRNA cis splicing, via spliceosome / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / zinc 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: 3.02 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)314,27245
Polymers313,09527
Non-polymers1,17718
Water00
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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-43 kcal/mol
Surface area15340 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-41 kcal/mol
Surface area14620 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-73 kcal/mol
Surface area15320 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-45 kcal/mol
Surface area15630 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-37 kcal/mol
Surface area14390 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-41 kcal/mol
Surface area15390 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-43 kcal/mol
Surface area14680 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-71 kcal/mol
Surface area14480 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)34,9195
Polymers34,7883
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-39 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.823, 255.101, 94.112
Angle α, β, γ (deg.)90.000, 101.125, 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: 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*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: 3.53 Å3/Da / Density % sol: 70.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaCitrate (pH 6.0), 10% PEG 35000 / PH range: 5.6 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→48.86 Å / Num. obs: 84760 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 68.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17
Reflection shellResolution: 3.02→3.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4562 / CC1/2: 0.727 / % 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: 3.02→38.41 Å / SU ML: 0.4538 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8302
RfactorNum. reflection% reflection
Rfree0.2487 4114 4.86 %
Rwork0.2146 --
obs0.2162 84653 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.62 Å2
Refinement stepCycle: LAST / Resolution: 3.02→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17445 945 18 0 18408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218921
X-RAY DIFFRACTIONf_angle_d0.510625742
X-RAY DIFFRACTIONf_chiral_restr0.03812692
X-RAY DIFFRACTIONf_plane_restr0.00423242
X-RAY DIFFRACTIONf_dihedral_angle_d16.08192879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.060.45011450.3812726X-RAY DIFFRACTION100
3.06-3.090.38541390.35432758X-RAY DIFFRACTION99.93
3.09-3.130.35141390.31612838X-RAY DIFFRACTION99.9
3.13-3.170.36961550.30252695X-RAY DIFFRACTION99.96
3.17-3.220.28211190.27922814X-RAY DIFFRACTION100
3.22-3.260.37261430.27992767X-RAY DIFFRACTION100
3.26-3.310.34351530.28342753X-RAY DIFFRACTION100
3.31-3.360.32211750.27262781X-RAY DIFFRACTION99.97
3.36-3.420.33321510.26882694X-RAY DIFFRACTION99.93
3.42-3.480.31421520.2792838X-RAY DIFFRACTION99.97
3.48-3.540.26561290.26122736X-RAY DIFFRACTION99.97
3.54-3.610.32721140.24092831X-RAY DIFFRACTION100
3.61-3.680.27411390.23772729X-RAY DIFFRACTION100
3.68-3.760.26331370.2342845X-RAY DIFFRACTION100
3.76-3.850.25031390.23312733X-RAY DIFFRACTION100
3.85-3.950.24171310.22892808X-RAY DIFFRACTION100
3.95-4.050.26861320.22882784X-RAY DIFFRACTION100
4.05-4.170.26661130.20692772X-RAY DIFFRACTION100
4.17-4.310.22621430.19912818X-RAY DIFFRACTION100
4.31-4.460.21451570.18992768X-RAY DIFFRACTION99.97
4.46-4.640.22261490.1892733X-RAY DIFFRACTION100
4.64-4.850.21431480.18392796X-RAY DIFFRACTION100
4.85-5.10.20461210.17892785X-RAY DIFFRACTION100
5.1-5.420.21181420.17852797X-RAY DIFFRACTION99.86
5.42-5.840.2031750.17872762X-RAY DIFFRACTION99.93
5.84-6.420.19471520.1882768X-RAY DIFFRACTION100
6.42-7.350.26121530.18552789X-RAY DIFFRACTION100
7.35-9.240.18131280.16722820X-RAY DIFFRACTION100
9.24-38.410.20011410.1662801X-RAY DIFFRACTION99.26

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