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- PDB-6lbj: Structure of mouse GLD-2 (Terminal nucleotidyltransferase 2, TENT2) -

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Basic information

Entry
Database: PDB / ID: 6lbj
TitleStructure of mouse GLD-2 (Terminal nucleotidyltransferase 2, TENT2)
ComponentsPoly(A) RNA polymerase GLD2
KeywordsTRANSFERASE / mRNA processing / 5'-3' RNA polymerase activity / DNA polymerase type-B-like family / Terminal nucleotidyltransferase 2
Function / homology
Function and homology information


negative regulation of miRNA catabolic process / 5'-3' RNA polymerase activity / : / adenylyltransferase activity / : / RNA stabilization / dark adaptation / histone mRNA catabolic process / polynucleotide adenylyltransferase / : ...negative regulation of miRNA catabolic process / 5'-3' RNA polymerase activity / : / adenylyltransferase activity / : / RNA stabilization / dark adaptation / histone mRNA catabolic process / polynucleotide adenylyltransferase / : / hematopoietic progenitor cell differentiation / nucleotidyltransferase activity / hippocampus development / neuron differentiation / mRNA processing / retina development in camera-type eye / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) RNA polymerase GLD2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.70444053571 Å
AuthorsMa, X.Y. / Gao, S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing.
Authors: Ma, X.Y. / Zhang, H. / Feng, J.X. / Hu, J.L. / Yu, B. / Luo, L. / Cao, Y.L. / Liao, S. / Wang, J. / Gao, S.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(A) RNA polymerase GLD2
B: Poly(A) RNA polymerase GLD2


Theoretical massNumber of molelcules
Total (without water)84,7462
Polymers84,7462
Non-polymers00
Water54030
1
A: Poly(A) RNA polymerase GLD2


Theoretical massNumber of molelcules
Total (without water)42,3731
Polymers42,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) RNA polymerase GLD2


Theoretical massNumber of molelcules
Total (without water)42,3731
Polymers42,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.277, 47.144, 105.446
Angle α, β, γ (deg.)87.381, 88.056, 63.806
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSchain 'A'AA146 - 22130 - 105
12THRTHRALAALAchain 'A'AA233 - 479117 - 363
23GLUGLULYSLYS(chain 'B' and (resid 146 through 221 or resid 233 through 480))BB146 - 22130 - 105
24THRTHRALAALA(chain 'B' and (resid 146 through 221 or resid 233 through 480))BB233 - 479117 - 363

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Components

#1: Protein Poly(A) RNA polymerase GLD2 / Terminal nucleotidyltransferase 2 / mGLD-2 / PAP-associated domain-containing protein 4


Mass: 42372.859 Da / Num. of mol.: 2 / Mutation: D213A, D279A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tent2, Gld2, Papd4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q91YI6, polynucleotide adenylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 23.6% PEG 3350, 80mM HEPEs pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.918003 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918003 Å / Relative weight: 1
ReflectionResolution: 2.7→42.28 Å / Num. obs: 17614 / % possible obs: 88.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 67.3048882299 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1695 / CC1/2: 0.835 / % possible all: 83.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JNB

5jnb


Resolution: 2.70444053571→35.5139056296 Å / SU ML: 0.504284643462 / Cross valid method: FREE R-VALUE / σ(F): 1.95855275381 / Phase error: 37.2259755908
RfactorNum. reflection% reflection
Rfree0.270837041836 925 5.77223088924 %
Rwork0.252858949368 --
obs0.253956762327 16025 80.3378954229 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 91.2178284413 Å2
Refinement stepCycle: LAST / Resolution: 2.70444053571→35.5139056296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 0 30 5322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008278653766775404
X-RAY DIFFRACTIONf_angle_d1.162172789237309
X-RAY DIFFRACTIONf_chiral_restr0.0816148036006829
X-RAY DIFFRACTIONf_plane_restr0.00613584896334928
X-RAY DIFFRACTIONf_dihedral_angle_d19.86604148362055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.70444053571-2.8470.4130190900921440.3888747020962239X-RAY DIFFRACTION83.2634521314
2.847-3.02520.4272427562421320.3630573035912548X-RAY DIFFRACTION93.7718684395
3.0252-3.25870.3681799071611500.3485696867242443X-RAY DIFFRACTION91.399365527
3.2587-3.58630.388125009331010.3489064548371840X-RAY DIFFRACTION68.3691440648
3.5863-4.10460.283231545513790.2772991631631341X-RAY DIFFRACTION50.1235439463
4.1046-5.16880.2243351864561270.1938161839942321X-RAY DIFFRACTION85.1182197497
5.1688-35.5130.2133083974441920.1922100430662368X-RAY DIFFRACTION90.1408450704
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)
12.31068725952-2.20183880155-0.1775015730875.344573322133.032195506159.82669426782-0.2003216988450.1535138757630.3563825101020.8585471910770.1499680217020.171493665601-1.551109208330.2799574366520.09766743227241.08209664116-0.06237152302250.1756560656670.4928549390160.07244614865630.5899437986169.3336556894568.5637024987-78.0998793455
25.68620355304-2.11019895363-1.597130797596.27510293263-0.4329548380088.86079563830.0802392197474-0.00721336640861-0.342376588241-0.497151959644-0.144824745667-0.5915054402521.242297574061.06757259527-0.0008002018621770.5905761714210.1818837518920.003283476931340.7654361753660.04790642574510.45795058543417.307239074251.1974646332-85.4309913913
32.22159487292-1.44404568342-0.9296238753267.9584199388-0.3894952438466.872012531750.4732954126880.130639836540.0976476090770.421620527243-0.734364120608-0.5056682578010.8818221055381.632238062060.2312414791030.5698677760470.0690764468226-0.1338870570770.930604356331-0.04146923431730.45233129919319.571748518156.4944123991-83.9497402663
40.8436431685231.36861068210.7714103657019.27711382496-0.552278053485.95003565751-0.1532823112260.22624624361-0.06511985657380.05845172579470.510930917580.625917417102-1.00684808148-0.0878330182104-0.377398598970.423598764133-0.001512430136650.1400490490830.4902147266060.0197577781260.384339315758.0301527132260.1112653909-67.1439908106
55.93615579533-1.85151190878-5.334208101736.138346952750.7799348356374.97444977158-0.04228898226811.37156957849-0.515251058609-0.630553466704-0.3467559547062.317719526590.104086610312-3.280500275791.738510788080.3598239434750.2538007195520.1109930802170.9456974747630.105916969031.07653628635-5.9161197988354.3370610369-72.3975634079
67.30587847613-1.932537236381.521825711795.642521356290.2760762418835.216150685490.439285619488-0.38368757432-0.6821633447251.170752521330.2624026050381.1415210177-0.888560594198-1.01294839044-0.3611347371080.8052150884630.332632965210.3886648888740.6472217598260.113443849320.5547488085423.067155149954.6120025002-58.3432781098
74.85084336134-0.6678895774640.1372342556946.42967239424-1.511250544595.93675658833-0.341854193924-0.284264185810.144437955231.055302339680.635564931523-0.228494118178-1.061835603691.90342326957-0.2267711870890.957138297816-0.1103494008480.05679752650180.907526589704-0.01533243028230.38160841127915.327894532860.2258496037-57.5841126202
86.04812934015-0.443525514212-0.2551540550497.706642576223.313525451148.77431179323-0.908689723413-0.308100195705-1.15841582721-1.167614646420.2161618144420.8028970902512.399636881-0.7182814383390.4580512388781.6151742904-0.361503143152-0.1934800831890.881900886270.2191653530160.8021357711442.1440592191344.8283863192-125.838418451
96.684441300710.809261929330.9454609175837.35071856388-1.46989965299.049836499870.0252991051088-0.107359527680.3252754580650.5534243085050.2083487005270.190820570804-1.448456230010.913577334179-0.2300892412130.672717354271-0.09044994275050.09144369407990.5747576596040.02691425137120.35448772549510.413904550867.8162141665-106.413423646
107.26585054292-5.18696975256.772240615354.77465175839-4.451226645826.461468591870.7036449793781.123877426820.608336851464-0.115923423324-1.70360553216-0.824778045956-0.8260390534763.299403322781.209741092570.801115290257-0.34208148504-0.1038538739381.642134464360.1986631221050.65498393881520.869465318969.4767517738-108.316076462
110.140644568072-0.07423996222450.6152675600491.65089618211-2.686982229649.282841446760.05325986749230.09106740556930.0445632763969-0.3477599478160.3018631071480.3700556108310.7720414817390.068982760305-0.3530777526150.487436266972-0.0688522586111-0.05300655474290.470378768213-0.00194965728640.4909222871186.8220917995360.8992847427-118.696107527
125.120651385221.43225095575-0.907640735565.39503523659-1.088392191029.330816692180.03706441862710.2276551720280.585787349666-0.3579228383080.3725197647811.071774777970.966695380804-0.879165891048-0.152681513760.371913578084-0.190123902887-0.1461162366990.4509964168120.1162372413510.626982353333-0.74790637401165.3678388946-126.451459425
138.395025932742.622208961433.993294463473.103661484921.816186602052.11272795315-0.385451226559-0.9292263551120.4219439363860.575690802885-0.1827437317161.993944096151.01621502926-2.602586473121.612860877090.634116980382-0.6023043308840.0414424113951.119141969050.6761256289861.49827119102-10.802974355457.3595103873-122.977794568
144.333813620812.2907813329-0.5160676830035.12515146821-0.8896943539290.297559160856-0.2360938641040.4942832941340.430887515342-0.894521657860.7600846687570.4902332957831.91795061328-1.21219344953-0.1676752625961.44900193968-0.333099410261-0.3043512570130.713692382760.2114672722320.5837040785111.661631310663.5097760209-138.695766236
153.42444760243-2.66215013593-1.607790014316.909974711051.170647737643.09666563584-0.198970773530.4620555592111.54342304098-0.24006913030.3895115669960.324214077312-1.753021029980.762969751909-0.1504279217080.724230432503-0.188170721587-0.08743331840550.6793555496070.1282683325950.7981822914895.3894668865476.6377292142-132.936426086
166.516602443173.76807310717-2.518717934367.32171986201-2.871094415432.13667772085-0.5427648735650.847947248659-0.502354030898-0.6931156035860.9355243975390.4925652995361.483011902590.906898806754-0.3253312245511.592368068910.2649178213370.03013010147380.906443752874-0.0824133095650.57717431598614.194949048154.3668694484-139.164743765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 342 )
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 371 )
6X-RAY DIFFRACTION6chain 'A' and (resid 372 through 431 )
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 480 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 170 )
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 248 )
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 265 )
11X-RAY DIFFRACTION11chain 'B' and (resid 266 through 317 )
12X-RAY DIFFRACTION12chain 'B' and (resid 318 through 368 )
13X-RAY DIFFRACTION13chain 'B' and (resid 369 through 386 )
14X-RAY DIFFRACTION14chain 'B' and (resid 387 through 414 )
15X-RAY DIFFRACTION15chain 'B' and (resid 415 through 447 )
16X-RAY DIFFRACTION16chain 'B' and (resid 448 through 481 )

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