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- PDB-3mdi: Crystal Structure of the 25kDa Subunit of Human Cleavage factor I... -

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Basic information

Entry
Database: PDB / ID: 3mdi
TitleCrystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • RNA (5'-R(*UP*GP*UP*AP*AP*A)-3')
KeywordsRNA binding/RNA / CPSF5 / CF Im / mRNA processing / cleavage factor / Nudix protein / protein-RNA complex / RNA binding protein / RNA binding-RNA complex
Function / homology
Function and homology information


positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / protein heterotetramerization / Processing of Capped Intron-Containing Pre-mRNA / protein tetramerization / centriolar satellite / histone deacetylase binding / mRNA processing / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA / Cleavage and polyadenylation specificity factor subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYang, Q. / Gilmartin, G.M. / Doublie, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.
Authors: Yang, Q. / Gilmartin, G.M. / Doublie, S.
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
C: RNA (5'-R(*UP*GP*UP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6035
Polymers54,4193
Non-polymers1842
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-25 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.362, 72.037, 96.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Pre-mRNA cleavage factor Im 25 kDa subunit / Nucleoside diphosphate-linked moiety X motif 21 / Nudix motif 21


Mass: 26259.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM25, CPSF25, CPSF5, NUDT21 / Plasmid: His6-MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809
#2: RNA chain RNA (5'-R(*UP*GP*UP*AP*AP*A)-3')


Mass: 1900.197 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 25% PEG 8000, 0.2M Sodium phosphate pH 4.9, 0.1M Sodium acetate pH 5.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2009 / Details: mirrors
RadiationMonochromator: MAR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.074
ReflectionResolution: 2.07→20 Å / Num. obs: 30752 / % possible obs: 99.511 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.081 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.82
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 35077 / Num. unique all: 6307 / Num. unique obs: 6086 / % possible all: 87.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BHO

3bho


Resolution: 2.07→19.937 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.821 / Cross valid method: THROUGHOUT / σ(F): 1.55 / Stereochemistry target values: TWIN_LSQ_F / Details: Twin law: k,h,-l, Twin percentage 0.074
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3808 6.56 %RANDOM
Rwork0.18 ---
obs0.183 30752 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.575 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 67.27 Å2 / Biso mean: 26.139 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.135 Å2-0 Å20 Å2
2--0.796 Å2-0 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.07→19.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 126 12 277 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063618
X-RAY DIFFRACTIONf_angle_d1.134949
X-RAY DIFFRACTIONf_chiral_restr0.07539
X-RAY DIFFRACTIONf_plane_restr0.005618
X-RAY DIFFRACTIONf_dihedral_angle_d17.2311382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.1070.3171890.2762584277389
2.107-2.1450.2651880.2362698288693
2.145-2.1860.2551920.2282749294193
2.186-2.2310.281900.2192715290593
2.231-2.2790.3211850.2182690287594
2.279-2.3320.2891930.2212726291993
2.332-2.390.2491750.2162754292994
2.39-2.4550.291910.2132721291293
2.455-2.5270.2581930.2072692288593
2.527-2.6080.2811890.2032728291794
2.608-2.7010.2631870.1972710289794
2.701-2.8090.2641840.2042739292394
2.809-2.9360.2551940.1972701289593
2.936-3.0910.2231960.1842738293493
3.091-3.2830.2151860.1722717290394
3.283-3.5350.2151840.1642728291294
3.535-3.8880.2321920.1452721291393
3.888-4.4440.1781880.1292726291494
4.444-5.5730.1681960.1292702289893
5.573-18.5820.2131980.1792712291093

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