[English] 日本語
Yorodumi
- PDB-5yd0: Crystal structure of Schlafen 13 (SLFN13) N'-domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yd0
TitleCrystal structure of Schlafen 13 (SLFN13) N'-domain
ComponentsSchlafen 8Ufo361 discography
KeywordsHYDROLASE / Endonuclease / tRNA / rRNA / Anti-HIV
Function / homology
Function and homology information


: / replication fork arrest / tRNA decay / rRNA catabolic process / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of DNA replication / site of DNA damage / RNA endonuclease activity / defense response to virus / tRNA binding ...: / replication fork arrest / tRNA decay / rRNA catabolic process / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of DNA replication / site of DNA damage / RNA endonuclease activity / defense response to virus / tRNA binding / Hydrolases; Acting on ester bonds / DNA damage response / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Schlafen group 3-like, DNA/RNA helicase domain / Schlafen group 3, DNA/RNA helicase domain / Schlafen family / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Schlafen family member 13
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.182 Å
AuthorsYang, J.-Y. / Gao, S.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81772977, 31722016, 31470729 China
Ministry of Science and Technology (China)2013CB910500 China
Natural Science Foundation of Guangdong Province2014TQ01R584, 2014A030312015 China
CitationJournal: Nat Commun / Year: 2018
Title: Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control
Authors: Yang, J.Y. / Deng, X.Y. / Li, Y.S. / Ma, X.C. / Feng, J.X. / Yu, B. / Chen, Y. / Luo, Y.L. / Wang, X. / Chen, M.L. / Fang, Z.X. / Zheng, F.X. / Li, Y.P. / Zhong, Q. / Kang, T.B. / Song, L.B. ...Authors: Yang, J.Y. / Deng, X.Y. / Li, Y.S. / Ma, X.C. / Feng, J.X. / Yu, B. / Chen, Y. / Luo, Y.L. / Wang, X. / Chen, M.L. / Fang, Z.X. / Zheng, F.X. / Li, Y.P. / Zhong, Q. / Kang, T.B. / Song, L.B. / Xu, R.H. / Zeng, M.S. / Chen, W. / Zhang, H. / Xie, W. / Gao, S.
History
DepositionSep 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 27, 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: Schlafen 8
B: Schlafen 8
C: Schlafen 8
D: Schlafen 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,7988
Polymers164,5364
Non-polymers2624
Water362
1
A: Schlafen 8
C: Schlafen 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3994
Polymers82,2682
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Schlafen 8
D: Schlafen 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3994
Polymers82,2682
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.968, 134.065, 77.587
Angle α, β, γ (deg.)90.00, 105.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Schlafen 8 / Ufo361 discography / Schlafen family member 13


Mass: 41134.000 Da / Num. of mol.: 4 / Fragment: UNP residues 14-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slfn13, Slfn8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5U311
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Description: large and fragile cuboid, sensitive to cryo-protectant
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 20% PEG6000, 850-950 mM lithium chloride
PH range: 6.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 28393 / % possible obs: 99.2 % / Redundancy: 3.41 % / Net I/σ(I): 17.08
Reflection shellResolution: 3.18→3.38 Å / Redundancy: 3.36 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 4511 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.182→35.236 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1427 5.06 %
Rwork0.2003 --
obs0.2027 28212 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.182→35.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10295 0 4 2 10301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310482
X-RAY DIFFRACTIONf_angle_d0.63514080
X-RAY DIFFRACTIONf_dihedral_angle_d11.6846419
X-RAY DIFFRACTIONf_chiral_restr0.0451556
X-RAY DIFFRACTIONf_plane_restr0.0041792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1825-3.29620.43111320.33782528X-RAY DIFFRACTION94
3.2962-3.4280.33791370.26852720X-RAY DIFFRACTION100
3.428-3.58390.29761390.25582668X-RAY DIFFRACTION100
3.5839-3.77260.32851300.23892714X-RAY DIFFRACTION100
3.7726-4.00870.25751380.21262685X-RAY DIFFRACTION100
4.0087-4.31770.25611430.18922716X-RAY DIFFRACTION100
4.3177-4.75130.23341480.16762672X-RAY DIFFRACTION100
4.7513-5.43660.22361520.17872722X-RAY DIFFRACTION100
5.4366-6.84140.29131400.2262698X-RAY DIFFRACTION100
6.8414-35.23770.19441680.16912662X-RAY DIFFRACTION97
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)
12.02035.8091-0.46764.33821.74783.80150.3743-0.4970.3582-0.0717-0.4485-1.3721-0.77920.1231-0.2720.99190.0561-0.07450.80770.14240.868398.449534.962742.6258
28.5063-4.5163.01832.8246-1.82928.42790.3947-0.62470.0781-0.95540.5338-0.1455-0.7155-0.6172-0.93710.66170.0478-0.0180.5848-0.0871.020398.245553.602931.9558
36.4213-1.6817-2.80965.4813-0.4394.64220.20731.9936-0.5959-0.05050.36240.69650.0924-0.9069-0.51480.64430.00510.10531.3704-0.12671.220596.219744.172433.7443
47.95441.17941.10327.7718-1.18994.99410.38783.2289-0.1689-1.29250.4129-0.7435-0.40550.1067-0.27421.06730.22330.11621.5181-0.19941.1393109.056546.543125.9387
52.39092.9606-0.4958.6791-0.56314.5053-0.0475-0.2645-2.2635-0.6938-0.1788-0.84820.2684-0.1067-0.1770.9988-0.0042-0.03690.9125-0.23731.0947107.243641.177333.7907
66.2271-1.1224-1.66762.2962-0.47694.1668-0.72550.4623-1.8647-0.86520.3691-1.02920.81840.52410.36781.04690.11930.2530.8987-0.13941.3334125.293758.445126.8814
74.7823-4.06861.9698.8264-0.55843.68050.47130.77381.5326-1.7983-0.8866-2.090.12010.40320.41280.96470.04330.38430.90760.20661.2852126.747483.448621.5025
88.7179-1.52461.28034.561-1.96425.0554-0.05890.1635-0.3805-1.3122-0.0262-1.1492-0.2890.3540.18760.6731-0.01060.19870.7967-0.05470.8943121.250478.047925.3097
91.6612-0.15721.87973.4798-0.82724.70450.0813-0.01720.43640.3004-0.2467-1.083-0.69640.28270.22380.620.05450.13650.80990.02761.0517125.54179.278733.6547
103.16623.3423-3.99033.8915-5.539.74060.9602-0.8460.23241.31180.1080.2618-0.4594-0.0219-1.25551.0194-0.0229-0.1351.03540.07371.1772119.850851.642842.8139
119.7213-3.07831.68597.0898-6.14368.916-0.6140.32930.0504-0.68230.4828-0.97970.84141.32670.2330.62750.1142-0.0091.1202-0.26970.7164104.432187.070745.0759
125.16360.6768-1.62469.519-1.62154.5201-0.31820.154-0.8926-0.52360.2320.64911.1139-0.42560.14390.6671-0.0227-0.04120.6853-0.05420.607793.878283.742931.5564
133.486-5.64384.14067.7851-5.34867.95260.13540.84860.1963-0.2883-0.56-0.43910.0960.8830.47460.5232-0.08760.08050.8509-0.05570.582997.832499.23421.9474
149.31541.71230.26567.22951.3487.2341-0.00670.94930.3869-0.64520.26960.2171-0.06630.236-0.27810.52880.05050.0180.55940.05830.482371.825105.95383.4239
154.05422.21874.17282.88552.44627.16-0.1212-0.76221.06450.0599-0.27750.5588-0.4565-0.94960.41580.59940.04970.04610.70830.03070.705370.0539110.42612.5357
166.7506-0.55822.13082.53451.1261.8043-0.032-0.16060.33730.9588-0.0294-0.3105-0.6536-0.3151-0.21770.8151-0.0206-0.08960.93-0.09670.656792.1312108.183732.1606
174.1315-5.4883-0.81788.3681-1.27389.57360.29231.1985-0.7438-0.2464-0.6955-0.34330.1244-0.81570.50260.8788-0.11250.07390.9612-0.19151.585749.209642.770223.727
187.02881.2555-1.08766.6654-0.49725.45870.2371-0.04370.23130.5135-0.3136-0.1752-0.32470.64170.04680.7102-0.03410.01560.7172-0.09070.906566.218844.196518.2353
198.5938-5.9082-3.6617.3466-1.75538.0967-0.18150.9411-0.37820.30870.5762-0.00150.56510.52450.27870.688-0.0627-0.03080.8988-0.2951.012458.47536.756614.834
206.5758-2.26922.84937.22160.042.4740.85141.1558-0.6647-1.1287-0.43121.47080.7837-0.7794-0.24291.3020.067-0.11691.1338-0.20940.904879.091522.54879.6652
211.5372-0.53361.19440.81040.36585.2355-0.1341.2449-1.4081-0.91880.3051-1.65080.52472.54950.00991.7482-0.0590.73071.8636-0.4132.2699106.297516.895212.8125
226.59421.93976.17183.07410.80646.0853-0.93891.2920.3597-0.7626-0.08710.0441-0.68570.96951.30631.075-0.01540.22970.8411-0.01541.235597.183727.014217.7545
234.10983.75750.36294.1486-1.72753.2242-0.1722-0.0792-1.3251-0.1013-0.1915-0.715-0.05590.590.23260.95710.06020.15170.8828-0.28741.524595.177319.698421.653
246.8828-2.356-4.7661.89990.83649.15860.50430.76651.86791.3899-0.2941-0.7999-0.1888-0.4069-0.16870.9562-0.12370.17890.85780.17671.607766.387822.085422.951
257.66782.7361-4.583.3208-0.87085.6910.22810.07120.384-1.1086-0.0426-0.4001-0.96790.8798-0.04960.830.03920.03650.80550.02240.669156.940595.33727.3712
266.5237-1.0176-0.34287.8137-0.89029.0242-0.47440.1597-0.2654-0.48840.0833-1.11520.43340.88440.34620.6665-0.03730.07890.71750.06580.652561.447981.149916.0684
273.83224.4011.43638.95237.64438.2409-0.06120.1764-0.357-0.58240.2379-0.09560.2996-0.383-0.14280.7602-0.1473-0.14370.88470.09750.590552.822780.63687.192
284.025-3.7528-0.26347.40751.33224.3768-0.04310.5296-0.6277-1.3208-0.03450.88860.0726-0.01530.05431.1754-0.4317-0.1530.9531-0.10140.724244.930652.5346-2.1903
295.9471.63562.23149.45515.80183.7526-0.2217-0.5462-0.1859-0.8243-0.50821.2727-0.9312-0.50620.58850.9956-0.2034-0.19920.813-0.05860.774339.126478.625912.0466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 158 )
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 218 )
8X-RAY DIFFRACTION8chain 'A' and (resid 219 through 254 )
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 327 )
10X-RAY DIFFRACTION10chain 'A' and (resid 328 through 351 )
11X-RAY DIFFRACTION11chain 'B' and (resid -2 through 19 )
12X-RAY DIFFRACTION12chain 'B' and (resid 20 through 75 )
13X-RAY DIFFRACTION13chain 'B' and (resid 76 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 254 )
15X-RAY DIFFRACTION15chain 'B' and (resid 255 through 327 )
16X-RAY DIFFRACTION16chain 'B' and (resid 328 through 351 )
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 19 )
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 94 )
19X-RAY DIFFRACTION19chain 'C' and (resid 95 through 124 )
20X-RAY DIFFRACTION20chain 'C' and (resid 125 through 158 )
21X-RAY DIFFRACTION21chain 'C' and (resid 159 through 200 )
22X-RAY DIFFRACTION22chain 'C' and (resid 201 through 236 )
23X-RAY DIFFRACTION23chain 'C' and (resid 237 through 327 )
24X-RAY DIFFRACTION24chain 'C' and (resid 328 through 350 )
25X-RAY DIFFRACTION25chain 'D' and (resid -3 through 19 )
26X-RAY DIFFRACTION26chain 'D' and (resid 20 through 94 )
27X-RAY DIFFRACTION27chain 'D' and (resid 95 through 143 )
28X-RAY DIFFRACTION28chain 'D' and (resid 144 through 327 )
29X-RAY DIFFRACTION29chain 'D' and (resid 328 through 351 )

+
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