[English] 日本語
Yorodumi
- PDB-4oi4: Protein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454... -

+
Open data


ID or keywords:

Loading...

-
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 ...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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 254 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more