[English] 日本語
Yorodumi
- PDB-6lbj: Structure of mouse GLD-2 (Terminal nucleotidyltransferase 2, TENT2) -

+
Open data


ID or keywords:

Loading...

-
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


RNA polyadenylation at postsynapse / negative regulation of miRNA catabolic process / perforant pathway to dendrate granule cell synapse / regulation of translation at postsynapse / histone mRNA catabolic process / target-directed miRNA degradation / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / positive regulation of protein targeting to membrane ...RNA polyadenylation at postsynapse / negative regulation of miRNA catabolic process / perforant pathway to dendrate granule cell synapse / regulation of translation at postsynapse / histone mRNA catabolic process / target-directed miRNA degradation / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / positive regulation of protein targeting to membrane / postsynaptic modulation of chemical synaptic transmission / hematopoietic progenitor cell differentiation / postsynapse / glutamatergic synapse / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more