[English] 日本語
Yorodumi
- PDB-8syk: Crystal structure of RNA device 43 truncation mutant 3 (U100C), h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8syk
TitleCrystal structure of RNA device 43 truncation mutant 3 (U100C), holo state
ComponentsRNA device 43 truncation mutant 3 (U100C)
KeywordsRNA / RNA device / aptazyme / tetracycline riboswitch / ribozyme
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / TETRACYCLINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsStagno, J.R. / Deme, J.C. / Lee, Y.-T. / Wang, Y.-X. / Lee, H.K. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.
Authors: Jason R Stagno / Justin C Deme / Vibha Dwivedi / Yun-Tzai Lee / Hyun Kyung Lee / Ping Yu / Szu-Yun Chen / Lixin Fan / Maximilia F S Degenhardt / Raj Chari / Howard A Young / Susan M Lea / Yun-Xing Wang
Abstract: Synthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here, we present multidisciplinary structural and ...Synthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here, we present multidisciplinary structural and biochemical data for a tetracycline (Tc)-responsive RNA device (D43) in both ligand-free and bound states, providing a structure-dynamical basis for signal transmission. Activation of self-cleavage is achieved via ligand-induced conformational and dynamical changes that stabilize the elongated bridging helix harboring the communication module, which drives proper coordination of the catalytic residues. We then show the utility of CRISPR-integrated D43 in EL4 lymphocytes to regulate programmed cell death protein 1 (PD-1), a key receptor of immune checkpoints. Treatment of these cells with Tc showed a dose-dependent reduction in PD-1 by immunostaining and a decrease in messenger RNA levels by quantitative PCR as compared with wild type. PD-1 expression was recoverable upon removal of Tc. These results provide mechanistic insight into RNA devices with potential for cancer immunotherapy or other applications.
History
DepositionMay 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA device 43 truncation mutant 3 (U100C)
B: RNA device 43 truncation mutant 3 (U100C)
C: RNA device 43 truncation mutant 3 (U100C)
D: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,42073
Polymers138,0674
Non-polymers5,35369
Water37821
1
A: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,99524
Polymers34,5171
Non-polymers1,47823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,77615
Polymers34,5171
Non-polymers1,25914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,87319
Polymers34,5171
Non-polymers1,35618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,77615
Polymers34,5171
Non-polymers1,25914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.223, 81.223, 528.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: RNA chain
RNA device 43 truncation mutant 3 (U100C)


Mass: 34516.688 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-TAC / TETRACYCLINE


Mass: 444.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H24N2O8 / Comment: medication, antibiotic*YM
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.05 M HEPES pH 7.5, 0.01 M MgCl2, 2.5 mM Spermine, 14% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.06→528.84 Å / Num. obs: 35158 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.095 / Χ2: 0.98 / Net I/σ(I): 10.8 / Num. measured all: 427293
Reflection shellResolution: 3.06→3.21 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 2.148 / Num. measured all: 58097 / Num. unique obs: 4553 / CC1/2: 0.464 / Rpim(I) all: 0.625 / Rrim(I) all: 2.239 / Χ2: 0.95 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→44.32 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 1770 5.06 %
Rwork0.2249 --
obs0.2266 35012 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 168.2 Å2
Refinement stepCycle: LAST / Resolution: 3.06→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 9392 61 21 9474
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONf_bond_d0.001105090.085
X-RAY DIFFRACTIONf_angle_d0.48163860.217
X-RAY DIFFRACTIONf_dihedral_angle_d15.1755233
X-RAY DIFFRACTIONf_chiral_restr0.0252175
X-RAY DIFFRACTIONf_plane_restr0.002463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.140.40741250.37452491X-RAY DIFFRACTION100
3.14-3.240.3371250.28842511X-RAY DIFFRACTION100
3.24-3.340.28831040.28912509X-RAY DIFFRACTION100
3.34-3.460.26611260.26752498X-RAY DIFFRACTION100
3.46-3.60.31041190.26182534X-RAY DIFFRACTION100
3.6-3.760.29361370.23862500X-RAY DIFFRACTION100
3.76-3.960.25711440.23942521X-RAY DIFFRACTION100
3.96-4.210.29321450.23472519X-RAY DIFFRACTION100
4.21-4.530.26841710.24562528X-RAY DIFFRACTION100
4.53-4.990.26291380.22792551X-RAY DIFFRACTION100
4.99-5.710.24141490.22482591X-RAY DIFFRACTION100
5.71-7.190.29481390.24282646X-RAY DIFFRACTION100
7.19-44.320.22391480.18872843X-RAY DIFFRACTION100
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)
10.24870.0855-0.2890.0544-0.42360.4135-0.3979-0.3226-0.4957-0.54150.1537-0.09640.7571-0.35750.34731.1395-0.1635-0.32831.73140.24970.903149.8543-38.076524.1518
22.14330.77861.56160.06150.44220.57870.74670.0797-1.07260.351-0-0.47420.60490.2286-0.4611.2812-0.3425-0.35942.04090.35861.087134.5422-47.949720.9748
34.0661-1.25883.63493.6069-0.98793.29570.7483-0.96210.6725-0.09762.2141-0.6001-1.7349-0.8016-0.88091.4442-0.38310.26111.8576-0.34540.99551.5602-43.828713.5829
43.8313-0.8504-1.75842.50650.44381.4663-0.5743-0.193-1.74150.2701-0.91141.39770.8278-0.04030.88981.7248-0.5906-0.09381.62310.33931.6404-1.6797-66.575611.4983
55.35991.22711.95671.31440.45611.28020.2274-0.6261-1.35040.66690.8581-0.58380.5346-0.919-0.80911.2282-0.3407-0.33922.11890.37061.225931.8095-46.688112.7209
62.6708-0.86570.88741.2891-0.98030.9406-1.2171-0.5791-0.6515-0.73450.1145-1.5042-0.75740.2710.56971.03770.0399-0.12681.24310.30311.156463.9858-34.948935.2178
70.3738-0.52030.25423.2936-0.51790.9871-1.064-0.9789-0.1943-0.4180.26330.1042-0.29550.26630.17960.6331-0.55630.47351.78880.2171.926262.9492-7.237431.6111
83.15791.5557-0.16850.7785-0.07680.0077-0.9262-0.1851-0.44420.11330.47490.41810.5778-0.53040.04831.8767-0.70330.33122.13470.05642.84457.9144-22.461755.2472
94.8793-0.2028-0.91732.1827-0.83214.0537-0.7885-0.58490.094-1.11640.71320.96581.5846-0.6639-0.421.271-0.3884-0.1011.57470.51482.563551.6318-14.21938.048
103.4142-2.0818-3.30525.5193.34334.0653-0.0529-1.68270.7246-0.82080.9763-1.9508-1.6091.81011.08621.2273-0.22990.52722.54711.13241.948926.9243-41.506952.8654
112.45160.95641.35842.03241.95672.1086-0.5105-1.9878-0.0528-0.1889-0.3163-0.75550.05871.61570.43880.77960.02550.01452.79250.55411.438610.3319-37.2356.1562
120.8244-0.4126-0.12753.075-0.09411.28780.3364-0.53731.6761-0.8229-0.5912-0.42591.6973-0.863-0.42441.0342-1.17740.16381.80110.32441.825463.3035-9.825343.185
130.20450.1322-0.51661.2469-0.51220.5314-0.4336-0.10561.12410.1070.3741-0.7064-0.1004-0.0902-0.10451.0902-0.4519-0.15021.12530.65511.87863.981-24.473321.3663
144.02411.7341-0.77433.9376-1.54673.57490.4665-0.22310.9923-0.2625-0.3377-1.4498-0.10320.7897-0.31361.5893-0.20790.23121.03580.35691.51712.5349-26.886327.5086
151.05391.6474-0.86161.755-0.7810.44140.5872-0.2870.45830.5048-0.56170.4041-0.62310.8233-0.15641.5858-0.4868-0.36171.31950.43121.646932.0845-5.586814.2924
160.835-0.04860.29780.90080.10542.1526-0.82860.2389-0.90790.112-1.16440.0809-0.49880.5292-2.58612.1111-0.5557-1.26072.26871.78680.418948.6334.27839.3956
171.6274-0.80510.0661.52860.2996-0.3723-0.9561-0.06220.6297-0.67330.39340.2583-0.13060.22650.50971.5028-0.3644-0.22671.09390.29581.722236.76593.283220.1
181.24151.5613-1.23982.6002-2.60592.96160.3450.17990.8137-0.68240.51790.0643-0.4913-0.1054-0.16471.9601-0.59040.27061.15730.91830.2966-3.4679-41.858529.9982
194.21730.03060.25432.88030.33512.4251-0.0914-1.0734-0.3425-0.794-0.3705-1.7927-0.27551.08630.45961.0637-0.0763-0.23481.2120.31221.95491.0241-72.141236.9179
201.72160.42350.40.26970.39760.7997-0.8223-0.79730.16570.01660.09520.5081-0.3107-0.09170.2262.1999-0.3678-0.5622.19820.93622.871719.2631-79.976354.0476
214.6874-1.38330.8820.7252-0.95612.0486-2.9411-0.13340.01050.35940.4116-1.3585-1.13961.02681.56181.5976-0.2313-0.10411.7570.44823.070618.5927-71.752542.8157
220.5796-0.94110.078.14851.81890.9426-0.6435-0.41220.105-0.62110.43262.59480.12670.3815-1.23171.10040.0673-0.47412.34911.17731.386754.5656-60.939260.466
231.37530.0089-0.64560.1042-0.36720.703-0.817-0.9755-0.442-0.81851.24781.06741.155-0.0301-0.01911.0155-0.64740.22141.47951.23162.134272.7707-58.015445.5197
243.0464-0.69460.3086-0.0222-0.4397-0.0668-0.84470.0913-2.5151-0.4999-0.0705-0.42150.0710.6901-1.68610.79820.452-0.12641.50920.85542.780822.3126-76.198748.4478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and (resid 201 or resid 9:30))
2X-RAY DIFFRACTION2(chain A and resid 31:54)
3X-RAY DIFFRACTION3(chain A and resid 55:63)
4X-RAY DIFFRACTION4(chain A and resid 64:92)
5X-RAY DIFFRACTION5(chain A and resid 93:108)
6X-RAY DIFFRACTION6(chain A and resid 109:115)
7X-RAY DIFFRACTION7(chain B and (resid 201 or resid 9:16))
8X-RAY DIFFRACTION8(chain B and resid 17:28)
9X-RAY DIFFRACTION9(chain B and resid 29:42)
10X-RAY DIFFRACTION10(chain B and resid 43:71)
11X-RAY DIFFRACTION11(chain B and resid 72:102)
12X-RAY DIFFRACTION12(chain B and resid 103:115)
13X-RAY DIFFRACTION13(chain C and (resid 201 or resid 9:27))
14X-RAY DIFFRACTION14(chain C and resid 28:37)
15X-RAY DIFFRACTION15(chain C and resid 38:61)
16X-RAY DIFFRACTION16(chain C and resid 62:75)
17X-RAY DIFFRACTION17(chain C and resid 76:110)
18X-RAY DIFFRACTION18(chain C and resid 111:115)
19X-RAY DIFFRACTION19(chain D and (resid 201 or resid 9:16))
20X-RAY DIFFRACTION20(chain D and resid 17:31)
21X-RAY DIFFRACTION21(chain D and resid 32:46)
22X-RAY DIFFRACTION22(chain D and resid 47:75)
23X-RAY DIFFRACTION23(chain D and resid 76:92)
24X-RAY DIFFRACTION24(chain D and resid 93:115)

+
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