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- PDB-4x4w: Crystal structure of the full-length human mitochondrial CCA-addi... -

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Basic information

Entry
Database: PDB / ID: 4x4w
TitleCrystal structure of the full-length human mitochondrial CCA-adding enzyme
ComponentsCCA tRNA nucleotidyltransferase 1, mitochondrial
KeywordsRNA BINDING PROTEIN / protein-RNA complex / tRNA / non-coding RNA / CCA-adding enzyme / nucleotidyltransferase / ncRNA
Function / homology
Function and homology information


5'-3' RNA polymerase activity / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / CCA tRNA nucleotidyltransferase / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / tRNA 3'-end processing / tRNA processing in the nucleus ...5'-3' RNA polymerase activity / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / CCA tRNA nucleotidyltransferase / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / tRNA 3'-end processing / tRNA processing in the nucleus / rescue of stalled ribosome / tRNA binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily ...: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / CCA tRNA nucleotidyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKuhn, C.-D. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2015
Title: On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme.
Authors: Kuhn, C.D. / Wilusz, J.E. / Zheng, Y. / Beal, P.A. / Joshua-Tor, L.
History
DepositionDec 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CCA tRNA nucleotidyltransferase 1, mitochondrial
B: CCA tRNA nucleotidyltransferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45023
Polymers95,7552
Non-polymers1,69521
Water15,006833
1
A: CCA tRNA nucleotidyltransferase 1, mitochondrial
hetero molecules

B: CCA tRNA nucleotidyltransferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45023
Polymers95,7552
Non-polymers1,69521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area4460 Å2
ΔGint-124 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.970, 142.360, 100.590
Angle α, β, γ (deg.)90.000, 94.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CCA tRNA nucleotidyltransferase 1, mitochondrial / Mitochondrial tRNA nucleotidyl transferase / CCA-adding / mt CCA-adding enzyme / mt tRNA CCA- ...Mitochondrial tRNA nucleotidyl transferase / CCA-adding / mt CCA-adding enzyme / mt tRNA CCA-diphosphorylase / mt tRNA CCA-pyrophosphorylase / mt tRNA adenylyltransferase


Mass: 47877.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRNT1, CGI-47 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q96Q11, CCA tRNA nucleotidyltransferase

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Non-polymers , 5 types, 854 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.2M Ammonium Sulfate, 0.05M Na Citrate pH 5.5 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 89161 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.55 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.059 / Χ2: 1.013 / Net I/σ(I): 15.69 / Num. measured all: 271414
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.7460.5362.3319696671266680.6599.3
1.95-20.8130.4352.8919961641763710.52399.3
2-2.060.8750.3343.7519488634162920.40299.2
2.06-2.120.9170.2544.818258609560240.30898.8
2.12-2.190.9430.2046.0817745593758680.24798.8
2.19-2.270.970.1547.7117573577957600.18699.7
2.27-2.360.9740.1348.8516587550354680.16299.4
2.36-2.450.9810.11610.1516762537753360.1499.2
2.45-2.560.9870.09511.715592513450770.11598.9
2.56-2.690.9890.08313.4214425486848020.10198.6
2.69-2.830.9930.06416.9214170463246010.07899.3
2.83-30.9960.0521.2413340442743930.0699.2
3-3.210.9970.03926.4412856415941170.04899
3.21-3.470.9980.03230.8811246386537860.03998
3.47-3.80.9990.02736.8210489354234760.03398.1
3.8-4.250.9990.02341.139260321731520.02898
4.25-4.910.9990.0244.798493283627760.02497.9
4.91-6.010.9990.02241.477004242523670.02697.6
6.01-8.50.9990.0242.585510186918330.02498.1
8.50.9990.01651.55295910439940.01995.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.076 Å / FOM work R set: 0.8902 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 4458 5 %
Rwork0.1539 84695 -
obs0.156 89153 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.84 Å2 / Biso mean: 32.81 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.9→29.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 153 833 7390
Biso mean--57.17 41.55 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176614
X-RAY DIFFRACTIONf_angle_d1.5728905
X-RAY DIFFRACTIONf_chiral_restr0.098985
X-RAY DIFFRACTIONf_plane_restr0.0091134
X-RAY DIFFRACTIONf_dihedral_angle_d13.7282527
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.26281480.22272815296399
1.9216-1.94420.23751500.20532861301199
1.9442-1.96790.23681470.20412794294199
1.9679-1.99280.23271480.19152811295999
1.9928-2.0190.24171490.19572821297099
2.019-2.04670.23231510.18342873302499
2.0467-2.07590.22851470.18622788293599
2.0759-2.10690.22961490.17292835298499
2.1069-2.13980.22491480.16142815296398
2.1398-2.17490.17871470.15542798294599
2.1749-2.21240.19551480.148527992947100
2.2124-2.25260.19531520.144528853037100
2.2526-2.29590.17121490.139628452994100
2.2959-2.34270.18191480.14662803295199
2.3427-2.39360.21441500.14262864301499
2.3936-2.44930.20021490.14952817296699
2.4493-2.51050.18411480.14562811295999
2.5105-2.57830.2291480.15072823297198
2.5783-2.65420.21521480.15182805295399
2.6542-2.73980.18841510.14682861301299
2.7398-2.83760.19971460.15242784293099
2.8376-2.95110.19391510.14682860301199
2.9511-3.08530.18061470.15282809295699
3.0853-3.24780.18491490.14792826297599
3.2478-3.45090.21041480.14252813296198
3.4509-3.71690.16561490.13872827297698
3.7169-4.090.13941470.13012800294798
4.09-4.67970.16691470.12642785293298
4.6797-5.88790.20621500.16222847299798
5.8879-29.07980.24551490.19762820296998
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)
12.1086-0.0379-0.49141.7279-0.17011.980.0386-0.06360.05010.0613-0.0356-0.0129-0.04430.04070.01920.12320.0077-0.00650.0995-0.00490.149925.276845.907674.7852
22.86591.05410.49941.79190.62751.1143-0.0425-0.08270.0867-0.00050.0559-0.0644-0.06390.0064-0.01220.16430.0379-0.01330.17450.03180.169828.273674.474664.6044
31.10411.1681.62392.79613.3484.1939-0.04630.0478-0.05260.24990.20410.0059-0.00990.3722-0.18440.35060.0104-0.01740.2739-0.03370.239256.396191.290884.1014
42.58640.69150.9332.16740.89451.728-0.04580.18250.0395-0.2072-0.0418-0.2206-0.17020.19510.08380.1948-0.01510.04260.17890.03410.240632.627198.486224.2749
52.26040.42370.68292.09870.02112.1444-0.00140.1354-0.226-0.19610.033-0.02620.06050.0525-0.00780.1689-0.01150.0060.1182-0.01470.186321.960492.529322.5953
64.16121.84891.48164.60470.72572.2114-0.0777-0.1364-0.05580.09830.045-0.0558-0.2308-0.04510.00540.2006-0.0150.00130.1810.05480.157922.212381.468239.389
72.7967-0.9883-0.73681.37460.46431.3283-0.06550.0328-0.07830.01880.0865-0.09420.04840.0831-0.02280.1598-0.02740.00120.17190.0180.196629.877262.220434.7552
83.5506-1.5914-3.18011.46491.43092.8321-0.14860.2369-0.1555-0.3662-0.08670.16110.2797-0.09230.2130.2967-0.00180.02160.2202-0.05940.222149.167754.627422.7041
93.3150.0256-1.03173.87422.17674.72420.0521-0.31190.1449-0.01160.293-0.2737-0.40810.9968-0.35960.413-0.0420.03950.4096-0.01910.214164.282141.00339.7719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 160 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 317 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 409 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 44 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 145 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 182 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 317 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 363 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 364 through 409 )B0

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