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- PDB-3c66: Yeast poly(A) polymerase in complex with Fip1 residues 80-105 -

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Basic information

Entry
Database: PDB / ID: 3c66
TitleYeast poly(A) polymerase in complex with Fip1 residues 80-105
Components
  • Poly(A) polymerase
  • Pre-mRNA polyadenylation factor FIP1
KeywordsTRANSFERASE / Peptide-protein complex / mRNA processing / Nucleus / RNA-binding / Phosphoprotein
Function / homology
Function and homology information


termination of RNA polymerase II transcription, poly(A)-coupled / sno(s)RNA 3'-end processing / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / mRNA processing / protein-macromolecule adaptor activity / magnesium ion binding / RNA binding ...termination of RNA polymerase II transcription, poly(A)-coupled / sno(s)RNA 3'-end processing / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / mRNA processing / protein-macromolecule adaptor activity / magnesium ion binding / RNA binding / ATP binding / nucleus
Similarity search - Function
Pre-mRNA polyadenylation factor Fip1 domain / : / Fip1 motif / 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 ...Pre-mRNA polyadenylation factor Fip1 domain / : / Fip1 motif / 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
Poly(A) polymerase / Pre-mRNA polyadenylation factor FIP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBohm, A. / Meinke, G.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein.
Authors: Meinke, G. / Ezeokonkwo, C. / Balbo, P. / Stafford, W. / Moore, C. / Bohm, A.
History
DepositionFeb 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Poly(A) polymerase
B: Poly(A) polymerase
C: Pre-mRNA polyadenylation factor FIP1
D: Pre-mRNA polyadenylation factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,08818
Polymers128,4894
Non-polymers1,59914
Water3,783210
1
A: Poly(A) polymerase
C: Pre-mRNA polyadenylation factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9008
Polymers64,2452
Non-polymers6566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-7 kcal/mol
Surface area25800 Å2
MethodPISA
2
B: Poly(A) polymerase
D: Pre-mRNA polyadenylation factor FIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,18810
Polymers64,2452
Non-polymers9438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-6 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.124, 184.211, 73.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly(A) polymerase / PAP / Polynucleotide adenylyltransferase


Mass: 61439.508 Da / Num. of mol.: 2 / Fragment: UNP residues 1-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAP1, YKR002W / Production host: Escherichia coli (E. coli)
References: UniProt: P29468, polynucleotide adenylyltransferase
#2: Protein/peptide Pre-mRNA polyadenylation factor FIP1


Mass: 2805.141 Da / Num. of mol.: 2 / Fragment: UNP residues 80-105 / Source method: obtained synthetically / References: UniProt: P45976
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM MjES pH 6.5, 9% Peg 20,000, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 47034 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.622 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 23.238 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 2382 5.1 %RANDOM
Rwork0.19722 ---
obs0.20024 44538 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8786 0 102 210 9098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229161
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.95912414
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.77751122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78724.115418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.838151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421560
X-RAY DIFFRACTIONr_chiral_restr0.1370.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026861
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.24286
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26275
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4841.55704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85829035
X-RAY DIFFRACTIONr_scbond_it1.28433874
X-RAY DIFFRACTIONr_scangle_it2.0654.53369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 167 -
Rwork0.304 3031 -
obs--94.2 %
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)
12.0691-0.3647-1.29273.7506-1.56234.75470.00960.02380.07440.47890.11520.1747-0.703-0.3936-0.12490.00640.1466-0.131-0.1628-0.049-0.3274-38.2932.4279.292
21.51330.10490.06782.7151-0.52691.8592-0.02910.18420.20040.3812-0.0427-0.4474-0.28610.37440.0718-0.2042-0.0666-0.11830.0094-0.0079-0.0448-24.1887.871-16.12
34.7448-0.7127-0.9133.1310.85912.45560.11640.05240.62070.163-0.03830.1449-0.233-0.1065-0.0781-0.1876-0.0081-0.0474-0.11860.0796-0.0722-52.50120.593-21.942
41.9988-0.85691.1342.6641-0.121.91810.1314-0.1182-0.3333-0.12180.11720.20330.2037-0.166-0.24860.0048-0.0399-0.0685-0.09540.0018-0.0904-29.761-31.232-48.705
51.8203-1.2081-0.14582.540.42021.36550.0111-0.12690.0082-0.13190.1542-0.41830.02870.3003-0.1653-0.23840.0032-0.054-0.0321-0.0564-0.0083-8.63-29.842-28.26
63.58850.35960.23376.32370.88813.73460.153-0.0656-0.25920.7439-0.20860.3233-0.0006-0.11870.0556-0.11250.04210.0644-0.17940.0885-0.1654-29.296-50.961-17.911
714.8479-0.7497-5.77822.29741.383716.7597-0.19731.3750.5749-0.61670.13950.56940.2361-0.64110.0578-0.19650.0012-0.12060.01980.1641-0.1385-60.07617.187-33.63
86.64791.9045-0.80867.15772.56085.8106-0.4946-1.2742-1.12171.50720.35320.5171-1.0847-0.75480.14130.48980.01470.3211-0.03380.1501-0.149-34.855-50.304-4.758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 19041 - 190
2X-RAY DIFFRACTION2AA3 - 403 - 40
3X-RAY DIFFRACTION2AA191 - 357191 - 357
4X-RAY DIFFRACTION3AA358 - 532358 - 532
5X-RAY DIFFRACTION4BB41 - 19041 - 190
6X-RAY DIFFRACTION5BB3 - 403 - 40
7X-RAY DIFFRACTION5BB191 - 357191 - 357
8X-RAY DIFFRACTION6BB358 - 531358 - 531
9X-RAY DIFFRACTION7CC80 - 1031 - 24
10X-RAY DIFFRACTION8DD80 - 1021 - 23

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