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- PDB-3nyb: Structure and function of the polymerase core of TRAMP, a RNA sur... -

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Basic information

Entry
Database: PDB / ID: 3nyb
TitleStructure and function of the polymerase core of TRAMP, a RNA surveillance complex
Components
  • Poly(A) RNA polymerase protein 2
  • Protein AIR2
KeywordsTRANSFERASE/RNA BINDING PROTEIN / polyA RNA polymerase / zinc knuckle protein / RNA surveillance / Mtr4p binds to Trf4p/Air2p heterodimer / TRANSFERASE-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


polyadenylation-dependent RNA catabolic process / polyadenylation-dependent ncRNA catabolic process / polyadenylation-dependent mRNA catabolic process / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / meiotic DNA double-strand break formation ...polyadenylation-dependent RNA catabolic process / polyadenylation-dependent ncRNA catabolic process / polyadenylation-dependent mRNA catabolic process / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / RNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / histone mRNA catabolic process / tRNA modification / negative regulation of DNA recombination / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair / protein-macromolecule adaptor activity / molecular adaptor activity / cell division / mRNA binding / nucleolus / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Poly(A) polymerase complex subunit Air1/2, budding yeast / Nucleotidyltransferase Trf4-like / : / : / AIR2-like, CCHC-type 1 zinc finger 4 / Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase ...Poly(A) polymerase complex subunit Air1/2, budding yeast / Nucleotidyltransferase Trf4-like / : / : / AIR2-like, CCHC-type 1 zinc finger 4 / Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Few Secondary Structures / Irregular / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Poly(A) RNA polymerase protein 2 / Protein AIR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7007 Å
AuthorsReinisch, K.M. / Hamill, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and function of the polymerase core of TRAMP, a RNA surveillance complex.
Authors: Hamill, S. / Wolin, S.L. / Reinisch, K.M.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Aug 14, 2019Group: Data collection / Category: computing
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 / 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_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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Poly(A) RNA polymerase protein 2
B: Protein AIR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9904
Polymers45,8592
Non-polymers1312
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-57 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.720, 92.720, 103.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Poly(A) RNA polymerase protein 2 / DNA polymerase sigma / DNA polymerase kappa / Topoisomerase 1-related protein TRF4


Mass: 36459.453 Da / Num. of mol.: 1
Fragment: central and catalytic domains of Trf4p (UNP residues 161-481)
Mutation: D293A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAP2, TRF4, YOL115W, O0716, HRC584 / Production host: Escherichia coli (E. coli)
References: UniProt: P53632, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Protein AIR2 / Arginine methyltransferase-interacting RING finger protein 2


Mass: 9399.759 Da / Num. of mol.: 1
Fragment: fourth and fifth zinc knuckles of Air2p (UNP residues 118-198)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: AIR2, YDL175C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12476
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28215 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2009
RadiationMonochromator: cryogenically cooled Si double crystal (111) monochromator
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 16163 / Num. obs: 16163 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.077
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.6-2.690.0822.30.86100
2.69-2.80.1094.30.64100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
SHARPphasing
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7007→24.656 Å / SU ML: 0.37 / σ(F): 0.14 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 979 6.94 %random
Rwork0.1935 ---
obs0.1982 14108 96.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.544 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0538 Å2-0 Å20 Å2
2---1.0538 Å2-0 Å2
3---2.1076 Å2
Refinement stepCycle: LAST / Resolution: 2.7007→24.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 2 58 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063152
X-RAY DIFFRACTIONf_angle_d1.0344260
X-RAY DIFFRACTIONf_dihedral_angle_d19.1271142
X-RAY DIFFRACTIONf_chiral_restr0.07464
X-RAY DIFFRACTIONf_plane_restr0.004546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7007-2.84290.32981060.24451727X-RAY DIFFRACTION89
2.8429-3.02080.30171380.23161774X-RAY DIFFRACTION93
3.0208-3.25350.33631410.23631845X-RAY DIFFRACTION97
3.2535-3.580.31371550.21591883X-RAY DIFFRACTION99
3.58-4.0960.2431490.17931916X-RAY DIFFRACTION100
4.096-5.15280.20531390.14461960X-RAY DIFFRACTION100
5.1528-24.6570.21481510.17582024X-RAY DIFFRACTION100
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)
11.2468-0.6808-0.7511.71380.19051.03540.04610.0256-0.2468-0.3362-0.1998-0.11110.08640.2312-0.11510.22450.05490.09860.18110.01110.171558.4413.7212-26.4413
20.76510.2214-0.42291.3288-0.0180.5820.0853-0.1517-0.0211-0.0871-0.1486-0.325-0.05930.1553-0.06630.0443-0.0578-0.01140.17450.05830.176664.887116.7498-1.5634
30.02770.0217-0.01190.02420.08910.04910.51090.6855-0.0929-0.4244-0.67260.36980.0695-0.1318-00.75650.08390.0480.4997-0.2570.39547.5781-2.6239-44.3231
40.1909-0.15690.17680.0797-0.06730.0111-0.14010.111-0.6752-0.8346-0.1662-0.32380.17380.4882-0.00030.7030.0820.260.4914-0.24630.568665.5754-7.4108-38.4191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESSEQ 159:189 OR RESSEQ 303:481
2X-RAY DIFFRACTION2RESSEQ 190:302
3X-RAY DIFFRACTION3RESSEQ 1122:1146 OR RESSEQ 2147
4X-RAY DIFFRACTION4RESSEQ 1160:1198 OR RESSEQ 2148

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