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- PDB-1f5a: CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE -

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Basic information

Entry
Database: PDB / ID: 1f5a
TitleCRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE
ComponentsPOLY(A) POLYMERASE
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 / cytosolic mRNA polyadenylation / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / manganese ion binding / magnesium ion binding ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / cytosolic mRNA polyadenylation / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / manganese ion binding / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Poly(A) polymerase / 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 nucleotidyltransferase 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, RNA-binding domain / Poly(A) polymerase, central domain / : / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(A) polymerase nucleotidyltransferase 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 (domestic 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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.

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Components

#1: Protein POLY(A) POLYMERASE


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 (domestic 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


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


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


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

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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: 2.73 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

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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

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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

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