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- PDB-2npi: Clp1-ATP-Pcf11 complex -

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Basic information

Entry
Database: PDB / ID: 2npi
TitleClp1-ATP-Pcf11 complex
Components
  • Protein CLP1
  • Protein PCF11
KeywordsTRANSCRIPTION / Clp1-Pcf11 complex / ATP binding / ternary complex
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 / Protein PCF11 / mRNA cleavage and polyadenylation factor CLP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsNoble, C.G. / Beuth, B. / Taylor, I.A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor
Authors: Noble, C.G. / Beuth, B. / Taylor, I.A.
History
DepositionOct 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: Protein CLP1
B: Protein CLP1
C: Protein PCF11
D: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3648
Polymers129,3014
Non-polymers1,0634
Water2,666148
1
A: Protein CLP1
C: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1824
Polymers64,6502
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-22 kcal/mol
Surface area19330 Å2
MethodPISA
2
B: Protein CLP1
D: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1824
Polymers64,6502
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-23 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.967, 94.993, 181.404
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 Protein CLP1


Mass: 52295.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CLP1 / Plasmid: pACYCDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08685
#2: Protein Protein PCF11 / protein 1 of CF I


Mass: 12355.019 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)
Description: co-expressed, recombinant material / Gene: PCF11 / Plasmid: pACYCDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39081
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2005 / Details: mirror
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. all: 33184 / Num. obs: 29786 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.112 / Net I/σ(I): 9.7
Reflection shellResolution: 2.95→3.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.444 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→15 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.817 / SU B: 41.679 / SU ML: 0.374 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30332 1493 5.1 %RANDOM
Rwork0.24757 ---
obs0.25042 28040 90.03 %-
all-31052 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7225 0 64 148 7437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.97510154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50724.683331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.186151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7721538
X-RAY DIFFRACTIONr_chiral_restr0.0760.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.23460
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25004
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2161.54613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.33927372
X-RAY DIFFRACTIONr_scbond_it0.43933226
X-RAY DIFFRACTIONr_scangle_it0.6594.52782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 68 -
Rwork0.373 1264 -
obs--57.76 %
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)
14.9655-0.35950.712110.03222.542113.3527-0.18770.71180.0504-0.68780.16290.2439-0.6093-0.18160.02480.269-0.0955-0.0308-0.1880.1238-0.294240.193927.694526.2549
21.2665-0.2637-0.87913.28181.40924.6580.00750.06550.0639-0.5659-0.09140.2428-0.4077-0.37880.0839-0.07920.0484-0.0864-0.1920.0286-0.171631.667623.109549.8356
34.51590.6975-1.3462.31790.00275.164-0.23810.358-0.5695-0.1458-0.03440.74711.6465-1.03310.27250.3019-0.257-0.0177-0.0361-0.07510.056524.9366-3.97447.4878
48.6559-0.3547-0.59764.0337-1.43939.20530.0429-0.86140.06980.3353-0.23510.0328-0.25830.3520.1922-0.31610.00790.0563-0.0337-0.0352-0.24234.113426.4991108.372
53.48130.13280.39940.99740.0182.7584-0.0438-0.16810.32330.0207-0.05020.0829-0.2106-0.25780.0939-0.22580.0115-0.0311-0.193-0.0185-0.150839.027934.812484.716
62.9922-0.64640.9584.0479-1.16264.7342-0.2264-0.1180.7275-0.01170.0408-0.4356-0.7690.88810.1856-0.1638-0.1177-0.0339-0.0598-0.03930.076763.834746.953288.9322
70.37420.57210.986312.38765.538111.37170.10760.4003-0.0216-0.04450.4719-0.28920.59120.8036-0.5795-0.0771-0.01140.0493-0.1250.0397-0.268944.03717.646752.2999
87.6127-0.63876.61531.31653.471618.58660.1687-0.1945-0.2727-0.0536-0.5215-0.10160.72580.49610.3528-0.2789-0.06870.0771-0.2019-0.0191-0.189857.247724.709286.1525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 10033 - 115
2X-RAY DIFFRACTION2AA101 - 341116 - 356
3X-RAY DIFFRACTION3AA342 - 445357 - 460
4X-RAY DIFFRACTION4BB18 - 10033 - 115
5X-RAY DIFFRACTION5BB101 - 341116 - 356
6X-RAY DIFFRACTION6BB342 - 445357 - 460
7X-RAY DIFFRACTION7CC477 - 49824 - 45
8X-RAY DIFFRACTION8DD475 - 49922 - 46

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