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- PDB-4dgw: Crystal Structure of the SF3a splicing factor complex of U2 snRNP -

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Basic information

Entry
Database: PDB / ID: 4dgw
TitleCrystal Structure of the SF3a splicing factor complex of U2 snRNP
Components
  • Pre-mRNA-splicing factor PRP11
  • Pre-mRNA-splicing factor PRP21
  • Pre-mRNA-splicing factor PRP9
KeywordsSPLICING / Zinc Finger
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding ...mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / mRNA 5'-splice site recognition / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / zinc ion binding / nucleus
Similarity search - Function
Immunoglobulin-like - #2690 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1320 / Surp module / Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal ...Immunoglobulin-like - #2690 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1320 / Surp module / Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / Zinc-finger of C2H2 type / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing factor PRP9 / Pre-mRNA-splicing factor PRP21 / Pre-mRNA-splicing factor PRP11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.112 Å
AuthorsLin, P.C.
CitationJournal: Embo J. / Year: 2012
Title: Structure and assembly of the SF3a splicing factor complex of U2 snRNP
Authors: Lin, P.C. / Xu, R.M.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor PRP9
B: Pre-mRNA-splicing factor PRP21
C: Pre-mRNA-splicing factor PRP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7254
Polymers89,6603
Non-polymers651
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-52 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.781, 127.259, 169.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Pre-mRNA-splicing factor PRP9


Mass: 48184.188 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P19736
#2: Protein Pre-mRNA-splicing factor PRP21


Mass: 18397.299 Da / Num. of mol.: 1 / Fragment: Middle domain, UNP residues 87-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P32524
#3: Protein Pre-mRNA-splicing factor PRP11


Mass: 23078.561 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 50-266 / Mutation: L153M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q07350
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAIN C IS RESIDUES 50-266 IN UNP DATABASE, PRP11_YEAST INCLUDING N-TERMINAL 14 ...THE SEQUENCE OF CHAIN C IS RESIDUES 50-266 IN UNP DATABASE, PRP11_YEAST INCLUDING N-TERMINAL 14 TAGS. (SEE BELOW) MGSSHHHHHHSQDPDQVRSNPYIYKNHSGKLVCKLCNTMH MSWSSVERHLGGKKHGLNVLRRGISIEKSSLGREGQTTHD FRQQQKIIEAKQSLKNNGTIPVCKIATVKNPKNGSVGLAI QVNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKG KKFLVIAYEPFENIAIELPPNEILFSENNDMDNNNDGVDE LNKKCTFWDAISKLYYVQFFFKQAEQEQADV THE AUTHOR COULD DETERMINE THE RESIDUES 149-253. THE AUTHOR COULD OBSERVE RESIDUES 101-136 AND BELIEVED THAT THESE RESIDUES IS PART OF THE N-TERMINAL RESIDUES 36-148. BUT THE AUTHOR IS NOT SURE WHICH PART CORRESPONDS WITH THESE RESIDUES. SO THE RESIDUE NUMBERS OF 101-136 IS MEANINGLESS.

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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: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8-12% Ethanol, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9791, 0.9794, 0.9600
SYNCHROTRONNSLS X29A20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 27, 2008
ADSC QUANTUM 3152CCDAug 23, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.961
40.97931
ReflectionResolution: 3.1→30 Å / Num. obs: 19171 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 94.38 Å2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.6 % / Num. unique all: 1618 / Rsym value: 0.467 / % possible all: 83

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.112→29.863 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7697 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1917 10 %RANDOM
Rwork0.2279 ---
all0.2329 ---
obs0.2329 19171 96.6 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.105 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 631.06 Å2 / Biso mean: 136.4866 Å2 / Biso min: 52.42 Å2
Baniso -1Baniso -2Baniso -3
1--11.5059 Å20 Å2-0 Å2
2--38.4954 Å20 Å2
3----26.9895 Å2
Refinement stepCycle: LAST / Resolution: 3.112→29.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 1 7 5195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085513
X-RAY DIFFRACTIONf_angle_d0.6257091
X-RAY DIFFRACTIONf_chiral_restr0.048759
X-RAY DIFFRACTIONf_plane_restr0.002918
X-RAY DIFFRACTIONf_dihedral_angle_d11.5842017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1115-3.22260.37661590.3281434159382
3.2226-3.35150.33451830.28571640182392
3.3515-3.50380.2471910.24471717190899
3.5038-3.68820.30171990.233317871986100
3.6882-3.91880.28661960.223417721968100
3.9188-4.22060.24891970.206217681965100
4.2206-4.64390.24781970.188317721969100
4.6439-5.31260.25122000.191718002000100
5.3126-6.6810.30852010.25118092010100
6.681-29.86390.28221930.23841747194092
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)
10.91140.3071-0.08240.9281-0.18640.7978-0.05410.3540.0722-0.25990.034-0.08730.03270.12120.03650.3947-0.022-0.00090.68450.11890.480614.223631.833158.2495
20.1805-0.31490.10021.0866-0.67510.64220.0355-0.18270.107-0.60730.3056-0.21050.4309-0.6021-0.27371.315-0.30730.17351.2149-0.02410.771458.431450.360631.4545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:378) OR (CHAIN B AND RESID 89:180)A0 - 378
2X-RAY DIFFRACTION1(CHAIN A AND RESID 0:378) OR (CHAIN B AND RESID 89:180)B89 - 180
3X-RAY DIFFRACTION2(CHAIN C AND RESID 101:253) OR (CHAIN B AND RESID 181:228)C101 - 253
4X-RAY DIFFRACTION2(CHAIN C AND RESID 101:253) OR (CHAIN B AND RESID 181:228)B181 - 228

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