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- PDB-3wfq: tRNA processing enzyme complex 1 -

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Basic information

Entry
Database: PDB / ID: 3wfq
TitletRNA processing enzyme complex 1
Components
  • Poly A polymerase
  • RNA (73-MER)
KeywordsTransferase/RNA / Terminal Nucleotide Transferase / Transferase-RNA complex
Function / homology
Function and homology information


CC tRNA cytidylyltransferase activity / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / nucleotide binding / metal ion binding
Similarity search - Function
: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. ...: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / CC-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciessynthetic construct (others)
Aquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.619 Å
AuthorsYamashita, S. / Takeshita, D. / Tomita, K.
CitationJournal: Structure / Year: 2014
Title: Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase
Authors: Yamashita, S. / Takeshita, D. / Tomita, K.
History
DepositionJul 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (73-MER)
B: RNA (73-MER)
C: RNA (73-MER)
D: RNA (73-MER)
E: Poly A polymerase
F: Poly A polymerase
G: Poly A polymerase
H: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)321,9528
Polymers321,9528
Non-polymers00
Water00
1
A: RNA (73-MER)
E: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)80,4882
Polymers80,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (73-MER)
F: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)80,4882
Polymers80,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (73-MER)
G: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)80,4882
Polymers80,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (73-MER)
H: Poly A polymerase


Theoretical massNumber of molelcules
Total (without water)80,4882
Polymers80,4882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.970, 154.030, 158.350
Angle α, β, γ (deg.)90.00, 107.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C
41chain D and segid D
12chain E and segid E
22chain F and segid F
32chain G and segid G
42chain H and segid H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
411chain D and segid DD0
112chain E and segid EE0
212chain F and segid FF0
312chain G and segid GG0
412chain H and segid HH0

NCS ensembles :
ID
1
2

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Components

#1: RNA chain
RNA (73-MER)


Mass: 23544.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 498539165
#2: Protein
Poly A polymerase


Mass: 56943.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: pcnB2 / Production host: Escherichia coli (E. coli)
References: UniProt: O67911, CCA tRNA nucleotidyltransferase
Sequence detailsTHE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW ...THE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW THE COMPLETE SEQUENCE. THE SEQUENCE OF RESIDUES 1-15 AND 449-512 (THE UNK PART) IS AS FOLLOWS. (1)MENIEIVSSGKHTLH(15), (449)EEIQKPLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTKNLKPLDEG(512) THE AUTHORS COULD OBSERVE A PART OF N- and C-TERMINAL RESIDUES (1-15 and 449-512, RESPECTIVLY) OF ALL PROTEIN CHAINS BUT THEY ARE NOT SURE WHICH PART CORRESPONDS WITH THESE OBSERVED RESIDUES. SO THE RESIDUE NUMBERS OF UNK ARE MEANINGLESS.

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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: 3.44 Å3/Da / Density % sol: 64.26 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorDate: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. obs: 27296

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFO, 3L0U

3wfo

3l0u


Resolution: 3.619→19.982 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.824 / SU ML: 0.56 / σ(F): 1.99 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2894 1361 5.03 %
Rwork0.2215 --
obs0.2249 27048 54.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 473.86 Å2 / Biso mean: 147.0686 Å2 / Biso min: 28.74 Å2
Refinement stepCycle: LAST / Resolution: 3.619→19.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13958 6180 0 0 20138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621130
X-RAY DIFFRACTIONf_angle_d0.80429939
X-RAY DIFFRACTIONf_chiral_restr0.0513581
X-RAY DIFFRACTIONf_plane_restr0.0042752
X-RAY DIFFRACTIONf_dihedral_angle_d12.2368727
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3483X-RAY DIFFRACTION9.22TORSIONAL
12B3483X-RAY DIFFRACTION9.22TORSIONAL
13C3483X-RAY DIFFRACTION9.22TORSIONAL
14D3483X-RAY DIFFRACTION9.22TORSIONAL
21E8043X-RAY DIFFRACTION9.22TORSIONAL
22F8043X-RAY DIFFRACTION9.22TORSIONAL
23G8043X-RAY DIFFRACTION9.22TORSIONAL
24H8043X-RAY DIFFRACTION9.22TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6187-3.74730.508780.24011701784
3.7473-3.89620.2794370.207148151811
3.8962-4.07210.2636390.22671040107922
4.0721-4.28480.2839950.22241671176636
4.2848-4.55030.27121190.20092233235247
4.5503-4.89690.26491480.20862800294860
4.8969-5.38090.29191730.20823452362573
5.3809-6.13970.30562300.25444326455692
6.1397-7.66220.34622530.254547495002100
7.6622-19.9820.26472590.20474765502499
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)
11.2650.27370.17083.0690.84043.2419-0.28191.3514-1.4287-0.82550.23540.99280.9832-1.8263-0.03831.2487-0.4718-0.23092.22730.01862.244715.0056-39.4745-5.2958
22.43582.3141-0.45682.94960.11471.1350.041-0.89251.14590.2462-0.43922.1309-0.8365-1.12180.27730.85290.39-0.81262.31920.15332.248216.219139.38155.5921
34.18981.41581.23750.71560.82911.34340.42921.0121-0.6590.33650.01020.31411.0088-1.472-0.49652.3058-0.46030.00182.0623-0.02111.9722-6.5806-57.680652.5599
40.44260.44430.60311.4050.10982.38260.23291.57971.0662-0.2045-0.39821.706-0.8816-1.33580.20562.0840.2915-0.13762.50760.56462.5889-9.196514.787552.2009
51.3685-0.4422-0.56412.6484-0.4342.2566-0.11220.0517-0.1018-0.81040.1951-0.54370.2964-0.0898-0.02240.1466-0.043-0.13880.466-0.02140.52146.1788-18.1485-0.0686
60.2997-0.04890.20561.87951.58141.5324-0.2418-0.5745-0.26291.17590.2834-1.5067-0.21371.0204-0.20991.5366-0.2895-0.76562.82270.4011.6516.4149-15.0975-30.8122
71.2382-0.0268-0.4082.41880.5722.41690.17190.03110.2205-0.35080.0197-0.4601-0.3188-0.0312-0.14830.20580.02370.02910.48060.10270.678946.981216.68051.3542
80.0884-0.50440.12713.2093-0.71260.1731-0.06380.26430.3079-0.4254-0.7208-1.0870.46530.51740.6621.9290.07920.65862.9675-0.02171.79467.05614.777331.3863
91.77230.3744-0.77452.1276-0.59882.5785-0.09350.0057-0.3681.51080.1115-0.07330.7429-0.16710.05652.1730.1268-0.05010.57010.15220.619523.6204-37.969774.0398
101.26111.12070.13631.15060.30340.2378-0.55891.2118-0.0617-1.3934-0.00760.85040.0523-0.67310.37361.2473-0.2964-0.28442.23440.04161.15429.8879-37.139526.6788
111.68820.2166-0.85222.62250.01282.78680.138-0.23980.27191.27720.04840.6894-0.0451-0.2057-0.15641.9660.03190.24060.62610.04580.690422.1659-3.35773.9075
120.7371-1.79320.34674.3616-0.83890.24510.0797-0.0243-0.5839-0.1122-0.2988-0.03080.5630.0530.24140.931-0.0991-0.13562.51930.0483.1677-27.816-6.07375.5664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:73)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:73)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 1:73)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 1:73)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 5:448)
6X-RAY DIFFRACTION6CHAIN E AND (RESSEQ 472:504)
7X-RAY DIFFRACTION7CHAIN F AND (RESSEQ 5:448)
8X-RAY DIFFRACTION8CHAIN F AND (RESSEQ 474:504)
9X-RAY DIFFRACTION9CHAIN G AND (RESSEQ 5:448)
10X-RAY DIFFRACTION10CHAIN G AND (RESSEQ 472:504)
11X-RAY DIFFRACTION11CHAIN H AND (RESSEQ 5:448)
12X-RAY DIFFRACTION12CHAIN H AND (RESSEQ 471:504)

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