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- PDB-6lbk: Structure of rat GLD-2 (Terminal nucleotidyltransferase 2, TENT2) -

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Basic information

Entry
Database: PDB / ID: 6lbk
TitleStructure of rat 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 / polynucleotide adenylyltransferase / histone mRNA catabolic process / : ...negative regulation of miRNA catabolic process / 5'-3' RNA polymerase activity / : / adenylyltransferase activity / : / RNA stabilization / dark adaptation / polynucleotide adenylyltransferase / histone mRNA catabolic process / : / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4956881144 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)87,6412
Polymers87,6412
Non-polymers00
Water70339
1
A: Poly(A) RNA polymerase GLD2


Theoretical massNumber of molelcules
Total (without water)43,8211
Polymers43,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) RNA polymerase GLD2


Theoretical massNumber of molelcules
Total (without water)43,8211
Polymers43,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.960, 40.720, 105.000
Angle α, β, γ (deg.)90.000, 100.204, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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
11THRTHRLYSLYS(chain 'A' and (resid 148 through 221 or resid 234 through 477))AA148 - 22144 - 117
12GLUGLULEULEU(chain 'A' and (resid 148 through 221 or resid 234 through 477))AA234 - 477130 - 373
23THRTHRLYSLYS(chain 'B' and resid 148 through 477)BB148 - 22144 - 117
24GLUGLULEULEU(chain 'B' and resid 148 through 477)BB234 - 477130 - 373

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Components

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


Mass: 43820.637 Da / Num. of mol.: 2 / Mutation: D279A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tent2, Gld2, Palp4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5U315, polynucleotide adenylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22.4% PEG 3350, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.49→47.2 Å / Num. obs: 44966 / % possible obs: 99.11 % / Redundancy: 6.5 % / Biso Wilson estimate: 60.3345537444 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.5
Reflection shellResolution: 2.4956881144→2.58 Å / Rmerge(I) obs: 0.524 / Num. unique obs: 23510 / CC1/2: 0.914

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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: 2.4956881144→47.1978941949 Å / SU ML: 0.338747606488 / Cross valid method: FREE R-VALUE / σ(F): 1.37375040396 / Phase error: 28.4211434675
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242530638455 2320 5.15945380954 %
Rwork0.204826722881 42646 -
obs0.206856945188 44966 99.1598121155 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.5432496443 Å2
Refinement stepCycle: LAST / Resolution: 2.4956881144→47.1978941949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 0 39 5274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01020899820485347
X-RAY DIFFRACTIONf_angle_d1.212930405567232
X-RAY DIFFRACTIONf_chiral_restr0.0706822640005819
X-RAY DIFFRACTIONf_plane_restr0.00808731702822918
X-RAY DIFFRACTIONf_dihedral_angle_d20.24929740182034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4957-2.54660.3770943145221370.2965785609662523X-RAY DIFFRACTION97.328942554
2.5466-2.6020.3207542540141190.2793278412422475X-RAY DIFFRACTION99.8076183147
2.602-2.66250.3331180115911410.2935614859762483X-RAY DIFFRACTION98.5725018783
2.6625-2.72910.3240225786971310.283852880422548X-RAY DIFFRACTION98.6013986014
2.7291-2.80290.3599605449221310.2772336384172492X-RAY DIFFRACTION99.3937097385
2.8029-2.88530.3654376140181210.2677905021972575X-RAY DIFFRACTION99.8888477214
2.8853-2.97850.3488678376861160.2608440629162492X-RAY DIFFRACTION99.5040061045
2.9785-3.08490.286376871370.2468784550932561X-RAY DIFFRACTION99.4471065241
3.0849-3.20840.2866394057341400.2341438593242470X-RAY DIFFRACTION99.5423340961
3.2084-3.35440.3153259414061460.2427557805742521X-RAY DIFFRACTION99.6264475159
3.3544-3.53120.2917222009331340.2237777916312506X-RAY DIFFRACTION99.0990990991
3.5312-3.75230.2881201233821530.2066336306672537X-RAY DIFFRACTION99.6296296296
3.7523-4.04190.2031200666021360.1762347921482506X-RAY DIFFRACTION99.8111069135
4.0419-4.44840.1445458605021390.1622899160872503X-RAY DIFFRACTION99.6981132075
4.4484-5.09140.182735727281510.1490194186882511X-RAY DIFFRACTION99.3654348638
5.0914-6.41210.2722440539861370.1885600391712483X-RAY DIFFRACTION98.830629951
6.4121-47.190.1971122571751510.1952723832312460X-RAY DIFFRACTION97.6439790576
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)
18.75785568122-0.143844883596-4.772711296381.79155624912-0.2748816103534.04732026646-0.5470232897980.734216394732-0.3398880843480.2856527378260.132446216556-0.499895719820.258491098783-0.2340346127280.2669838113490.5331284204350.0233077715266-0.0683098404120.7064342443990.04061877879780.47227427158851.782674743422.167525168886.9378135823
26.68244807024-3.44421560864-0.5938946243944.736252701284.034206758388.13774193654-0.1196477513340.284594328876-0.1968823899130.505544786988-0.3123975315160.1396025391150.203195851605-0.2993173600020.2513437213460.543875944881-0.007232581269520.08241111922950.6736994990790.1644922960650.40827232326437.433349373820.48932099889.8966729267
39.378323441430.0272361031475-2.117892952856.864830948041.924864437157.68082684763-0.2281134179910.6546283575740.715136739117-0.06704008357270.01199299673390.823443532938-1.76009467141-0.3282205579110.3702957879530.911592930060.258797073496-0.04169428649820.7031335990540.08006787579440.45539037958731.890153993831.131030669791.173442451
48.215332561191.13513818454-2.294284096155.03617442859-0.5538456070356.54102492942-0.497332831712-0.220431776628-0.6169519005940.1921594451210.115595659261-0.1090316182290.5889131140140.350917373550.3875289451850.365104959297-0.04360635155430.1283970828350.515738272727-0.01986166496540.45399052942246.181267588117.070616989873.7551115113
57.79479075511-0.806974160517-5.313402495726.88263732858-0.3074569896137.43016993908-1.16126100412-0.70636143831-2.445306878460.871672718897-0.217456623510.5837903872052.181652667120.7692182848471.362490907181.416590213230.1922209190070.369229109110.8954811131640.1506921631810.97786632819344.35175835153.7042600722881.2814709257
64.543054745380.6197828254022.359841464685.34241964218-2.608405631313.41813281716-0.3657785260441.44144439953-0.628424053942-0.824447704968-0.3269110293320.5375696900661.05554102916-1.182971442160.3580075947580.64212069732-0.2384722326450.07004265790211.40392296798-0.4715690477790.65616553890639.537316719614.593233123962.3310877698
77.181616497110.915666983154-1.333589581395.940454388761.72854293113.945727948860.4079058632472.06233098597-0.185687931349-0.348086282289-0.7487585971421.849008258890.319413055183-2.02428333704-0.08043907422420.407274331481-0.2266646732990.1100806309531.52228520482-0.3843747007820.98192143484632.601853585619.349700844668.7689356278
84.71099252443-1.802623427242.950181879647.136968513221.234015488595.653614695470.1330680515191.115874385931.91227483078-1.489279568220.0243812707624-0.791948403609-2.160100888420.456077676866-0.1165450802640.775514307195-0.1744247857780.07613814006491.147851049150.3040706177050.68700000250852.363752926428.698366965962.5829941505
97.727850223872.96862523806-5.171624922694.03592729209-2.101417849196.991774815040.07500769779520.34053885825-0.162250136406-0.482028205284-0.2207990738680.395307754811-0.0699743421824-1.19247800040.1258768027890.4646318029760.0522583573049-0.07456652282790.725878452747-0.2142442526790.47675944021236.708331067518.0130851188120.171238228
107.880222680820.5776729422380.005138085178327.67748001847-2.788283593126.73124087682-0.366418801555-0.2987434580921.25459540893-0.1244441252440.0695643058428-0.562650864772-1.66002413665-0.3452507879170.2994532384550.8777404294330.03238472894210.00263133786790.390200502284-0.1431588829370.49226164326748.23735042430.7582764079115.35569007
116.82165035945-2.11488716101-2.30023143544.06325714030.6806642906917.97090318776-0.1498322504460.506536801678-1.36365446115-0.337314669889-0.3437022141110.5382515312020.679312980185-0.4824724153590.2794098800360.378240126714-0.03991169134450.1088345508110.350890588865-0.09544936115020.64937951319139.355503530710.8827531419132.706027344
128.84817659127-2.61585565955-0.9414762848986.635615849881.181146200698.80106213953-0.169956866519-1.41574102550.08568310055170.690001465885-0.0567809477536-0.0340819613031-0.327083806730.3140247037750.1785623023460.519021041642-0.04500946116480.01597635327580.5430862270380.05543917304520.35963881825440.635052990620.0749809544145.193011237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 351 )
5X-RAY DIFFRACTION5chain 'A' and (resid 352 through 386 )
6X-RAY DIFFRACTION6chain 'A' and (resid 387 through 427 )
7X-RAY DIFFRACTION7chain 'A' and (resid 428 through 447 )
8X-RAY DIFFRACTION8chain 'A' and (resid 448 through 481 )
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 284 )
11X-RAY DIFFRACTION11chain 'B' and (resid 285 through 386 )
12X-RAY DIFFRACTION12chain 'B' and (resid 387 through 477 )

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