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- PDB-4c0h: Extended interface between Pcf11p and Clp1p and structural basis ... -

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Basic information

Entry
Database: PDB / ID: 4c0h
TitleExtended interface between Pcf11p and Clp1p and structural basis for ATP loss in Gly135Arg point mutant
Components
  • MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
  • PCF11P
KeywordsTRANSCRIPTION / 3' END MRNA PROCESSING / MUTANT
Function / homology
Function and homology information


polynucleotide 5'-hydroxyl-kinase activity / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / mRNA 3'-end processing / : / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding ...polynucleotide 5'-hydroxyl-kinase activity / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / mRNA 3'-end processing / : / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / Pcf11, Clp1-interaction domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain / Clp1, C-terminal domain superfamily ...Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / Pcf11, Clp1-interaction domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain / Clp1, C-terminal domain superfamily / Clp1, N-terminal beta-sandwich domain superfamily / Pre-mRNA cleavage complex II protein Clp1 / N-terminal beta-sandwich domain of polyadenylation factor / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Jelly Rolls / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pcf11p / Protein PCF11 / mRNA cleavage and polyadenylation factor CLP1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDupin, A.F. / Fribourg, S.
CitationJournal: Biochimie / Year: 2014
Title: Structural basis for ATP loss by Clp1p in a G135R mutant protein.
Authors: Dupin, A.F. / Fribourg, S.
History
DepositionAug 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen / reflns_shell
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
B: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
C: PCF11P
D: PCF11P


Theoretical massNumber of molelcules
Total (without water)125,3744
Polymers125,3744
Non-polymers00
Water45025
1
B: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
D: PCF11P


Theoretical massNumber of molelcules
Total (without water)62,6872
Polymers62,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-12.5 kcal/mol
Surface area19840 Å2
MethodPISA
2
A: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
C: PCF11P


Theoretical massNumber of molelcules
Total (without water)62,6872
Polymers62,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-12 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.395, 95.609, 182.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1 / CLP1P


Mass: 50378.664 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q08685
#2: Protein PCF11P


Mass: 12308.123 Da / Num. of mol.: 2 / Fragment: RESIDUES 454-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: N1P6M1, UniProt: P39081*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.1 Å3/Da / Density % sol: 60.36 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 43523 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 9.46 % / Biso Wilson estimate: 67.86 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.25
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 9.07 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 3.48 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.8 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9114 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.355 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2188 5.03 %RANDOM
Rwork0.1906 ---
obs0.1922 43472 99.66 %-
Displacement parametersBiso mean: 59.78 Å2
Baniso -1Baniso -2Baniso -3
1-4.9951 Å20 Å20 Å2
2---8.1411 Å20 Å2
3---3.146 Å2
Refine analyzeLuzzati coordinate error obs: 0.421 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 0 25 7319
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017474HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2410162HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2600SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1047HARMONIC5
X-RAY DIFFRACTIONt_it7474HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion20.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion997SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8036SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3086 127 4.18 %
Rwork0.2757 2909 -
all0.277 3036 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: 39.4756 Å / Origin y: 25.9623 Å / Origin z: 68.1305 Å
111213212223313233
T0.2399 Å20.0275 Å2-0.0296 Å2-0.1857 Å20.0149 Å2--0.2764 Å2
L0.7847 °20.2055 °20.2551 °2-0.952 °20.2964 °2--1.675 °2
S-0.1164 Å °-0.1022 Å °0.1254 Å °-0.319 Å °-0.0313 Å °0.0819 Å °-0.1173 Å °-0.1382 Å °0.1477 Å °
Refinement TLS groupSelection details: ALL

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