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- PDB-3pq1: Crystal structure of human mitochondrial poly(A) polymerase (PAPD1) -

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Basic information

Entry
Database: PDB / ID: 3pq1
TitleCrystal structure of human mitochondrial poly(A) polymerase (PAPD1)
ComponentsPoly(A) RNA polymerase
KeywordsTRANSFERASE / nucleotidyl transferase / RNP-type RNA binding domain / poly(A) polymerase / mitochondria
Function / homology
Function and homology information


mitochondrial RNA 3'-end processing / histone mRNA catabolic process / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / mRNA processing / manganese ion binding / intracellular membrane-bounded organelle / magnesium ion binding / protein homodimerization activity ...mitochondrial RNA 3'-end processing / histone mRNA catabolic process / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / mRNA processing / manganese ion binding / intracellular membrane-bounded organelle / magnesium ion binding / protein homodimerization activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
RL domain / RL domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) RNA polymerase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsBai, Y. / Srivastava, S.K. / Chang, J.H. / Tong, L.
CitationJournal: Mol.Cell / Year: 2011
Title: Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.
Authors: Bai, Y. / Srivastava, S.K. / Chang, J.H. / Manley, J.L. / Tong, L.
History
DepositionNov 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(A) RNA polymerase
B: Poly(A) RNA polymerase


Theoretical massNumber of molelcules
Total (without water)104,6612
Polymers104,6612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-32 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.680, 76.880, 87.630
Angle α, β, γ (deg.)90.00, 103.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESID 62:85 OR RESID 173:251 OR RESID...
211CHAIN B AND (RESID 62:85 OR RESID 173:251 OR RESID...

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Components

#1: Protein Poly(A) RNA polymerase / PAP / PAP-associated domain-containing protein 1 / Polynucleotide adenylyltransferase / Terminal ...PAP / PAP-associated domain-containing protein 1 / Polynucleotide adenylyltransferase / Terminal uridylyltransferase 1 / TUTase 1 / mtPAP


Mass: 52330.375 Da / Num. of mol.: 2 / Mutation: D325A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTPAP, PAPD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3)
References: UniProt: Q9NVV4, polynucleotide adenylyltransferase
Has protein modificationY
Sequence detailsAMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 44-538 IN UNIPROT DATABASE ENTRY Q9NVV4, PLUS A N- ...AMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 44-538 IN UNIPROT DATABASE ENTRY Q9NVV4, PLUS A N-TERMINAL EXPRESSION TAG (RESIDUES 23-43), WAS USED FOR CRYSTALLIZATION. MOST OF THE RESIDUES FROM RESIDUE 134 TO 172, AND FROM RESIDUE 452 TO 490 WERE MISSING IN THE COORDINATES DUE TO LACK OF ELECTRON DENSITY. SEVERAL RESIDUES WITHIN THESE RANGES WERE MODELED AS POLY-ALA SEGMENTS, AND ARE REPRESENTED AS UNK RESIDUES 151-157, 464-468, AND 474-478 OF CHAIN A, AND UNK RESIDUES 469-478 OF CHAIN B. THESE RESIDUE NUMBERS ARE ARBITRARILY ASSIGNED. IT IS EXPECTED THAT RESIDUES 151-157 BELONG TO THE 134-172 SEGMENT, AND RESIDUES 464-468 AND 474-478 BELONG TO THE 452-490 SEGMENT.

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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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: microbatch
Details: The precipitant solution contained 100 mM MES (pH 6.0), 6% (v/v) PEG4000, 35 mM NaCl, and 5 mM MgSO4. The protein was at 20 mg/mL concentration, and 0.5 mM MgATP was included as an additive. ...Details: The precipitant solution contained 100 mM MES (pH 6.0), 6% (v/v) PEG4000, 35 mM NaCl, and 5 mM MgSO4. The protein was at 20 mg/mL concentration, and 0.5 mM MgATP was included as an additive., microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96863, 0.97888, 0.97926
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.968631
20.978881
30.979261
ReflectionResolution: 3.1→30 Å / Num. obs: 30725 / % possible obs: 97.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9681
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.342 / % possible all: 90.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.1→28.912 Å / SU ML: 0.62 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3284 1436 4.95 %RANDOM
Rwork0.2473 ---
obs0.2514 28985 91.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.119 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.9378 Å2-0 Å2-12.5461 Å2
2---6.8323 Å2-0 Å2
3----3.102 Å2
Refinement stepCycle: LAST / Resolution: 3.1→28.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 0 0 5351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015438
X-RAY DIFFRACTIONf_angle_d1.3737317
X-RAY DIFFRACTIONf_dihedral_angle_d21.9721932
X-RAY DIFFRACTIONf_chiral_restr0.087829
X-RAY DIFFRACTIONf_plane_restr0.005932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2196X-RAY DIFFRACTIONPOSITIONAL
12B2196X-RAY DIFFRACTIONPOSITIONAL0.219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.21070.45591070.32642259X-RAY DIFFRACTION75
3.2107-3.3390.36551360.26252713X-RAY DIFFRACTION90
3.339-3.49080.36361270.23382753X-RAY DIFFRACTION91
3.4908-3.67450.32841430.2322744X-RAY DIFFRACTION91
3.6745-3.90420.29441440.23052769X-RAY DIFFRACTION93
3.9042-4.20480.3581600.2212718X-RAY DIFFRACTION91
4.2048-4.62640.29691640.21742879X-RAY DIFFRACTION96
4.6264-5.29230.31211400.21672896X-RAY DIFFRACTION97
5.2923-6.65420.34321640.26372928X-RAY DIFFRACTION98
6.6542-28.91340.25581510.25922890X-RAY DIFFRACTION96
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)
10.50920.0351-0.07620.8205-0.31620.47770.22-0.0697-0.09760.0912-0.14430.07090.05440.22240.00640.12930.01380.00030.07540.01510.113151.85864.4371-9.2333
21.0582-0.2286-0.07983.04130.53691.33640.2248-0.00560.13910.4914-0.1866-0.3195-0.03340.02840.04140.1279-0.06090.07890.1328-0.02140.080658.551837.89165.8891
30.92170.4410.12850.83340.85761.0302-0.27940.12680.0577-0.14050.16060.0396-0.50090.0178-0.02660.03510.00170.08980.1315-0.00410.050445.833523.1215-18.2128
40.59920.17240.34080.1465-0.09520.65010.06240.1779-0.3836-0.29310.2238-0.40410.12060.29950.05820.1608-0.0090.1470.1578-0.09780.490737.71399.0507-49.9837
50.64580.1174-0.46870.5642-0.56830.67840.1324-0.23520.3501-0.12540.04770.18880.1575-0.2714-0.00180.1669-0.07470.04110.19690.08310.17053.37011.7702-57.0675
60.9944-0.17930.33210.8399-0.34140.256-0.45940.5039-0.0407-0.48010.4345-0.25640.1254-0.35310.013-0.34540.3672-0.0588-0.2871-0.03850.126427.18477.1384-34.5681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 62:157
2X-RAY DIFFRACTION2CHAIN A AND (RESID 173:198 OR RESID 348:532)
3X-RAY DIFFRACTION3CHAIN A AND RESID 199:347
4X-RAY DIFFRACTION4CHAIN B AND RESID 62:130
5X-RAY DIFFRACTION5CHAIN B AND (RESID 173:198 OR RESID 348:532)
6X-RAY DIFFRACTION6CHAIN B AND RESID 199:347

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