[English] 日本語
Yorodumi
- PDB-5w0b: Structure of human TUT7 catalytic module (CM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w0b
TitleStructure of human TUT7 catalytic module (CM)
ComponentsTerminal uridylyltransferase 7
KeywordsTRANSFERASE / terminal uridyltransferase / TUTase
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA ...polyuridylation-dependent mRNA catabolic process / retrotransposon silencing by mRNA destabilization / uridylyltransferase activity / RNA 3'-end processing / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / oocyte maturation / miRNA binding / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 type domain signature. / Nucleotidyltransferase superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IODIDE ION / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.614 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114147 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis.
Authors: Faehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Terminal uridylyltransferase 7
B: Terminal uridylyltransferase 7
C: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,28414
Polymers134,1653
Non-polymers1,11911
Water39622
1
A: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9794
Polymers44,7221
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1375
Polymers44,7221
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terminal uridylyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1685
Polymers44,7221
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-134 kcal/mol
Surface area47330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.232, 141.232, 174.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resseq 987:995 or resseq 997 or resseq...
21(chain C and (resseq 987:995 or resseq 997 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resseq 987:995 or resseq 997 or resseq...B0
211(chain C and (resseq 987:995 or resseq 997 or resseq...C0

-
Components

#1: Protein Terminal uridylyltransferase 7 / TUT7 / TUTase 7 / Zinc finger CCHC domain-containing protein 6


Mass: 44721.812 Da / Num. of mol.: 3
Fragment: nucleotidyltransferase domain (UNP residues 983-1365)
Mutation: D1160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC6, HS2, KIAA1711, TUT7 / Plasmid: Multi-Bac, pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q5VYS8, RNA uridylyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
PH range: 5.0-6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 59600 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 66.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.8
Reflection shellResolution: 2.6→2.62 Å / Rmerge(I) obs: 0.597 / CC1/2: 0.828

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.614→61.155 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.255 3006 5.05 %
Rwork0.2305 --
obs0.2317 59520 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 378.23 Å2 / Biso mean: 95.1683 Å2 / Biso min: 37.7 Å2
Refinement stepCycle: final / Resolution: 2.614→61.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8361 0 39 22 8422
Biso mean--103.65 59.89 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038588
X-RAY DIFFRACTIONf_angle_d0.60311610
X-RAY DIFFRACTIONf_chiral_restr0.0421286
X-RAY DIFFRACTIONf_plane_restr0.0041475
X-RAY DIFFRACTIONf_dihedral_angle_d12.6065155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3486X-RAY DIFFRACTION5.793TORSIONAL
12C3486X-RAY DIFFRACTION5.793TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6135-2.65640.33181380.30642649278799
2.6564-2.70220.28871330.293527022835100
2.7022-2.75130.3031460.28726452791100
2.7513-2.80420.31911440.280426992843100
2.8042-2.86150.31611400.28926802820100
2.8615-2.92370.29761400.314426982838100
2.9237-2.99170.38431380.305127082846100
2.9917-3.06650.31061490.304926772826100
3.0665-3.14940.36471280.284726782806100
3.1494-3.24210.28671680.277626592827100
3.2421-3.34670.28161470.265827032850100
3.3467-3.46630.27141420.258726672809100
3.4663-3.60510.25191500.253727062856100
3.6051-3.76920.25411490.237926792828100
3.7692-3.96780.23771390.210726952834100
3.9678-4.21640.22331410.202327032844100
4.2164-4.54180.22231490.189527002849100
4.5418-4.99870.22571390.183327112850100
4.9987-5.72160.22581320.206227072839100
5.7216-7.20680.24421460.240127132859100
7.2068-61.1720.24141480.203627352883100
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)
15.49980.71963.4730.57710.69885.57960.0213-0.80750.55830.0514-0.31210.1221-0.2539-0.79520.22580.54010.07030.05980.3261-0.04940.52771.3808-50.877619.3572
23.49590.83284.71765.84244.10238.0601-0.0867-0.5721.33750.3022-0.41240.1893-0.398-0.19140.53640.6228-0.0685-0.03770.487-0.00580.636920.4008-43.314726.8117
39.75424.022-2.56644.3815-2.19639.0203-0.1947-0.39190.0071-0.17430.1526-0.38670.55980.52170.0150.5429-0.0059-0.06140.5815-0.07730.458725.1805-52.62729.2298
45.59010.61230.38375.8290.92053.9516-0.12580.11.01390.0069-0.0535-0.4906-0.77060.46170.1980.4893-0.0561-0.07980.44060.0670.49846.8752-41.15846.9116
53.99781.82344.19522.33965.48727.52930.3060.622-0.1609-0.74550.1759-1.4785-0.46031.1636-0.40080.5454-0.07340.09490.92120.13720.836819.7176-46.46452.4253
67.41370.937-1.01825.82-1.6724.7320.28030.3273-1.1309-0.3902-0.2234-0.09430.53340.1098-0.07760.51060.0918-0.05790.4962-0.0240.4625-0.2525-63.31974.2895
73.1613-3.19251.23926.9196-1.47812.99630.3037-0.22790.1776-0.98220.08580.44220.2886-0.4256-0.40450.4156-0.02350.06790.71910.05340.5229-7.2086-54.06639.1599
82.5679-0.51360.93874.33-3.38447.46520.03990.02960.11980.0353-0.3619-0.1876-0.25420.63930.35010.6007-0.04330.00650.68870.00450.42828.0243-65.6253.394
93.41211.2105-0.13783.1869-1.1194.87270.1388-0.5150.48570.5636-0.04010.2594-0.8677-0.1566-0.1090.7310.09430.04650.5214-0.11460.5727-5.1685-42.063748.0151
102.7471.7085-0.43756.5076-0.264.58820.11120.19610.47140.3948-0.00761.0003-0.6178-0.9477-0.02650.47830.08920.01330.70590.07960.5563-21.149-68.504128.7629
118.6323-4.340.45673.3531-0.01560.62550.00660.31620.00160.05660.0036-0.1290.25410.0244-0.02510.57-0.0205-0.00580.54030.07120.338312.0613-77.294718.6101
125.5357-1.47161.50712.08962.19954.83140.1211-0.4643-0.39970.08220.3827-0.26111.1610.0585-0.49980.86390.068-0.05360.85440.07890.62620.1715-81.811829.2078
136.51160.82182.60258.16825.58297.456-0.0643-0.3948-0.15350.9379-0.11610.47840.55260.39960.26010.43050.02350.02290.50580.03970.356212.6438-76.970126.5127
143.6214-1.6675-2.61015.40041.50111.76190.022-0.14440.06410.35110.0599-0.04260.22290.0883-0.09460.4942-0.09810.03660.48860.05210.3247-9.2835-80.33724.8988
153.9751-5.4572-1.68997.33732.52753.42150.04320.3518-0.2598-0.5262-0.2109-0.00490.4182-0.65560.1660.5966-0.17540.0610.5442-0.02860.4172-10.3632-88.56828.5594
164.307-1.7926-3.00944.49430.64796.5375-0.19270.97690.1271-0.3324-0.08980.82630.481-1.39090.25420.4102-0.1158-0.02210.77530.03090.5693-23.3453-78.954421.6318
176.91982.0819-2.6822.16960.29048.2667-0.6891-0.32-0.76780.18270.11181.05743.0016-0.89650.75271.1308-0.13930.14730.6630.13110.7117-17.9139-95.917224.7384
184.6063-3.8525-3.17886.88647.32268.319-0.0303-0.4392-0.48410.6510.66680.62051.0501-0.8587-0.7380.8172-0.01010.15740.58410.2070.5312-7.851-94.347327.9895
196.5898-3.56416.94783.678-2.53667.35680.4968-0.9301-0.0028-0.3925-0.35680.05160.66610.085-0.14960.9157-0.13730.25210.75950.16210.5342-18.279-81.923439.8799
202.36542.0176-4.27165.88421.98654.00940.346-0.59160.48031.8005-0.3310.9984-0.9397-0.32710.09180.8061-0.02230.07310.7556-0.15760.6381-18.3537-68.21540.8709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 985 through 1035 )B985 - 1035
2X-RAY DIFFRACTION2chain 'B' and (resid 1036 through 1075 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 1076 through 1126 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1127 through 1271 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1272 through 1293 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1294 through 1342 )B0
7X-RAY DIFFRACTION7chain 'A' and (resid 986 through 1035 )A986 - 1035
8X-RAY DIFFRACTION8chain 'A' and (resid 1036 through 1124 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1125 through 1361 )A0
10X-RAY DIFFRACTION10chain 'C' and (resid 986 through 1015 )C986 - 1015
11X-RAY DIFFRACTION11chain 'C' and (resid 1016 through 1076 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 1077 through 1105 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1106 through 1125 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1126 through 1183 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1184 through 1223 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 1224 through 1247 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 1248 through 1269 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 1270 through 1293 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 1294 through 1312 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 1313 through 1343 )C0

+
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://pdbjlvh1.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