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- PDB-4c0b: Structure of wild-type Clp1p-Pcf11p (454 -563) complex -

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Basic information

Entry
Database: PDB / ID: 4c0b
TitleStructure of wild-type Clp1p-Pcf11p (454 -563) complex
Components
  • MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
  • PCF11P
KeywordsTRANSCRIPTION / 3'-END MRNA PROCESSING
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
ADENOSINE-5'-TRIPHOSPHATE / 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: 2.77 Å
AuthorsFribourg, S. / Dupin, A.F.
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 1, 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 / Category: citation / 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 / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4938
Polymers125,4304
Non-polymers1,0634
Water79344
1
B: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
D: PCF11P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2464
Polymers62,7152
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-22.9 kcal/mol
Surface area19610 Å2
MethodPISA
2
A: MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
C: PCF11P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2464
Polymers62,7152
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-23.5 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.352, 95.410, 182.142
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: 50406.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: N1P6M1, UniProt: P39081*PLUS
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.53 Å3/Da / Density % sol: 65.18 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.77→40 Å / Num. obs: 40274 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 77.09 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 13.9
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 99.77

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NPI

2npi


Resolution: 2.77→40.55 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9067 / SU R Cruickshank DPI: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.409 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 2018 5.02 %RANDOM
Rwork0.1787 ---
obs0.1805 40190 99.59 %-
Displacement parametersBiso mean: 67.96 Å2
Baniso -1Baniso -2Baniso -3
1--5.734 Å20 Å20 Å2
2---1.7877 Å20 Å2
3---7.5218 Å2
Refine analyzeLuzzati coordinate error obs: 0.394 Å
Refinement stepCycle: LAST / Resolution: 2.77→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 64 44 7464
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3110328HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2636SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1085HARMONIC5
X-RAY DIFFRACTIONt_it7585HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion21.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1017SEMIHARMONIC5
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_contact8084SEMIHARMONIC4
LS refinement shellResolution: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2422 130 4.46 %
Rwork0.2223 2784 -
all0.2232 2914 -
obs--99.59 %
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)
10.799-0.52620.42292.42470.40233.8954-0.205-0.1785-0.08750.85630.07880.3787-0.0363-0.52570.1262-0.01010.02050.1549-0.20640.0379-0.2096-12.827-17.245546.1298
21.9288-0.1876-0.50430.71170.12361.4558-0.0530.3509-0.4142-0.0186-0.09640.05030.2762-0.14810.1495-0.2571-0.02120.0306-0.0636-0.1001-0.03590.0719-36.41790.3649
31.197-0.09920.93712.87372.13020.279-0.04330.0785-0.05910.24420.003-0.176-0.1290.09880.04030.1198-0.103-0.0083-0.08390.0707-0.06281.749-6.50341.7604
42.5319-0.5403-1.45021.58341.06932.1514-0.00610.1839-0.0031-0.0119-0.0373-0.0246-0.06710.05630.0434-0.21060.0008-0.00060.1322-0.01820.039216.0582-27.8250.0508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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