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- PDB-4oi4: Protein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454... -

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Basic information

Entry
Database: PDB / ID: 4oi4
TitleProtein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454deltaC563 of S. cerevisiae
Components
  • Protein PCF11
  • mRNA cleavage and polyadenylation factor CLP1
KeywordsTRANSCRIPTION / polynucleotide kinase / Clp1 / Pcf11 / cleavage factor Ia / 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 / RNA 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 / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Protein PCF11-like ...: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Protein PCF11-like / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDikfidan, A. / Loll, B. / Zeymer, C. / Clausen, T. / Meinhart, A.
CitationJournal: Mol.Cell / Year: 2014
Title: RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Authors: Dikfidan, A. / Loll, B. / Zeymer, C. / Magler, I. / Clausen, T. / Meinhart, A.
History
DepositionJan 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Structure summary
Revision 1.3Sep 20, 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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: mRNA cleavage and polyadenylation factor CLP1
C: mRNA cleavage and polyadenylation factor CLP1
B: Protein PCF11
D: Protein PCF11
U: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,43612
Polymers141,0965
Non-polymers1,3397
Water4,450247
1
A: mRNA cleavage and polyadenylation factor CLP1
B: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7595
Polymers64,1352
Non-polymers6243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-24 kcal/mol
Surface area19680 Å2
MethodPISA
2
C: mRNA cleavage and polyadenylation factor CLP1
D: Protein PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8516
Polymers64,1352
Non-polymers7164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-24 kcal/mol
Surface area19380 Å2
MethodPISA
3
U: Protein PCF11


Theoretical massNumber of molelcules
Total (without water)12,8261
Polymers12,8261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.640, 95.770, 181.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 5 molecules ACBDU

#1: Protein mRNA cleavage and polyadenylation factor CLP1


Mass: 51309.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CLP1, YOR250C / Plasmid: pGEM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: Q08685, polynucleotide 5'-hydroxyl-kinase
#2: Protein Protein PCF11 / protein 1 of CF I


Mass: 12825.654 Da / Num. of mol.: 3
Fragment: Clp1 interaction domain (UNP residues 454-563, SEE REMARK 999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PCF11, YDR228C, YD9934.13C / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P39081

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Non-polymers , 4 types, 254 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN U IS PART OF THE EXPRESSION TAG OF PCF11 THAT COULD NOT BE UNAMBIGUOUSLY ATTRIBUTED TO CHAIN B OR D.

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% w/v PEG6000, 100 mM Tris-HCl, pH 8.5, 18% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 61757 / Num. obs: 61162 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 57.2 Å2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.8 % / % possible all: 97.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NPI

2npi


Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.477 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22133 3061 5 %RANDOM
Rwork0.18698 ---
obs0.18873 58102 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.33 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 82 247 7624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.97710607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81724.816353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71151357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0451541
X-RAY DIFFRACTIONr_chiral_restr0.0750.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025824
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.22827
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25165
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4661.54834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76427665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14433371
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7754.52906
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 219 -
Rwork0.238 4215 -
obs--99.17 %
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)
17.3182-0.65370.59783.5609-0.97156.22880.038-1.10440.24370.5638-0.2069-0.0706-0.1541-0.12510.1689-0.2067-0.05040.04690.1919-0.0708-0.143333.658627.041108.2115
22.72390.22960.65210.89290.11772.6184-0.0605-0.20350.4026-0.0153-0.07770.162-0.3285-0.28640.1382-0.24520.0354-0.0172-0.1363-0.0634-0.110339.296835.243384.9603
32.8456-0.08651.40092.988-0.57843.9022-0.2407-0.0520.80890.0944-0.0272-0.399-0.86840.55780.2679-0.0868-0.1385-0.0779-0.0554-0.04220.178864.293447.342289.2723
43.27631.18912.17881.01382.78348.26860.1107-0.1667-0.23070.0319-0.1821-0.13510.61710.37050.0715-0.31310.02060.0003-0.1217-0.0088-0.093457.53625.12986.2402
54.59770.080.43526.7052-0.24758.4411-0.38160.5439-0.1019-1.42670.32750.344-0.4024-0.15880.05410.6259-0.1231-0.0743-0.12960.0914-0.182140.132828.098526.3923
61.17860.2913-0.50462.98781.16393.9794-0.0840.12030.1819-0.5699-0.09170.401-0.3609-0.51440.1757-0.03620.0622-0.0974-0.16870.029-0.148631.818723.002249.5564
73.5252-0.4909-1.2243.7491.92493.2216-0.23450.305-0.4862-0.0728-0.28020.80441.0858-0.91040.51470.3037-0.20820.0426-0.025-0.0810.047125.8024-4.412747.6654
80.58351.43952.56087.75915.849211.2915-0.2796-0.0445-0.145-0.47540.3898-0.71990.60191.0614-0.1103-0.02120.10790.0558-0.17310.0337-0.13645.28357.97651.6725
977.4355-31.90743.702463.9195-10.067839.98511.05173.9813-1.7179-4.2393-0.68452.09141.67410.0773-0.36720.0819-0.14110.01490.2349-0.08820.115423.671812.713476.2931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 102
2X-RAY DIFFRACTION2A103 - 342
3X-RAY DIFFRACTION3A343 - 445
4X-RAY DIFFRACTION4B475 - 499
5X-RAY DIFFRACTION5C19 - 102
6X-RAY DIFFRACTION6C103 - 342
7X-RAY DIFFRACTION7C343 - 445
8X-RAY DIFFRACTION8D476 - 499
9X-RAY DIFFRACTION9U451 - 458

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