[English] 日本語
Yorodumi
- PDB-1f5a: CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f5a
TitleCRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE
ComponentsPOLY(A) POLYMERASEPolynucleotide adenylyltransferase
KeywordsTRANSFERASE / mRNA processing / transcription / RNA-binding / phosphorylation / nuclear protein / alternative splicing helical turn motif / nucleotidyl transferase catalytic domain
Function / homology
Function and homology information


mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / cytosolic mRNA polyadenylation / : / manganese ion binding ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / cytosolic mRNA polyadenylation / : / manganese ion binding / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / TRIPHOSPHATE / : / Poly(A) polymerase alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsMartin, G. / Keller, W. / Doublie, S.
Citation
Journal: EMBO J. / Year: 2000
Title: Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
Authors: Martin, G. / Keller, W. / Doublie, S.
#1: Journal: Embo J. / Year: 1996
Title: Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.
Authors: Martin, G. / Keller, W.
#2: Journal: Protein Sci. / Year: 1999
Title: Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.
Authors: Martin, G. / Jeno, P. / Keller, W.
History
DepositionJun 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: POLY(A) POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3586
Polymers59,4441
Non-polymers9145
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.550, 62.720, 179.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein POLY(A) POLYMERASE / Polynucleotide adenylyltransferase


Mass: 59444.172 Da / Num. of mol.: 1
Fragment: C-TERMINAL DELETION MUTANT MISSING RESIDUES 514-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli)
References: UniProt: P25500, polynucleotide adenylyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, Ammonium sulfate, MES buffer, Calcium chloride, manganese chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
122 %(w/v)PEG80001reservoir
2100 mMMES1reservoir
3120 mMammonium sulfate1reservoir
45 mM1reservoirCaCl2
52 mM1reservoirMnCl2
62 mMbeta-mercaptoethanol1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONNSLS X12C10.9789
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDate
BRANDEIS1CCDOct 8, 1999
MARRESEARCH2IMAGE PLATEDec 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
21.54181
ReflectionResolution: 2.5→20 Å / Num. obs: 19890 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.67 Å / Rmerge(I) obs: 0.267 / % possible all: 65.1

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MHLH
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1368 7 %RANDOM
Rwork0.219 ---
all-19890 --
obs-19890 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.0537 Å2 / ksol: 0.352814 e/Å3
Displacement parametersBiso mean: 29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 46 168 3948
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.5→2.67 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.254
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.254

+
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