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- EMDB-21836: hc16 ligase -

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Basic information

Entry
Database: EMDB / ID: EMD-21836
Titlehc16 ligase
Map data
Sample
  • Complex: hc16 ligase
    • RNA: RNA (338-MER)
Keywordsribozyme / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsKappel K / Zhang K
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10 OD021600 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI145647 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832, R01GM079429, U54GM103297, R35 GM112579 United States
CitationJournal: Nat Methods / Year: 2020
Title: Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.
Authors: Kalli Kappel / Kaiming Zhang / Zhaoming Su / Andrew M Watkins / Wipapat Kladwang / Shanshan Li / Grigore Pintilie / Ved V Topkar / Ramya Rangan / Ivan N Zheludev / Joseph D Yesselman / Wah Chiu / Rhiju Das /
Abstract: The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve ...The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.
History
DepositionApr 20, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wlo
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21836.png

Downloads & links

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Map

FileDownload / File: emd_21836.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 224 pix.
= 239.68 Å		1.07 Å/pix.
x 224 pix.
= 239.68 Å		1.07 Å/pix.
x 224 pix.
= 239.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.03123029 - 0.09590831
Average (Standard dev.)0.0005406559 (±0.0050697075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 239.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z239.680239.680239.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0310.0960.001

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Supplemental data

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Sample components

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Entire : hc16 ligase

EntireName: hc16 ligase
Components
  • Complex: hc16 ligase
    • RNA: RNA (338-MER)

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Supramolecule #1: hc16 ligase

SupramoleculeName: hc16 ligase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RNA generated by in vitro transcription
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: RNA (338-MER)

MacromoleculeName: RNA (338-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 109.298711 KDa
SequenceString: GGUAGACUCG CAGGAAGUCU ACCGAGUAAG AGAAAGAGGA AAGACGGCCA AAUUGCGGGA AAGGGGACAA CAGCCGUUCA GUACCAAGU CUCAGGGAAA CUUCAGAUGG CCUCGCAAAG GGUAUGGUAA UAAGCUGACG GACAUGGUCC UAACCACGCA G UCAAGUCC ...String:
GGUAGACUCG CAGGAAGUCU ACCGAGUAAG AGAAAGAGGA AAGACGGCCA AAUUGCGGGA AAGGGGACAA CAGCCGUUCA GUACCAAGU CUCAGGGAAA CUUCAGAUGG CCUCGCAAAG GGUAUGGUAA UAAGCUGACG GACAUGGUCC UAACCACGCA G UCAAGUCC UAAGUCAACA GCCUUGGCUG UUGAUAUGGA UGCAUUUCGA UCCAACCGAG GCUCAUUCUU GUAAUUCAUG GC CGUCGGG GAGGCACUUC GGUGCCUCUG AUAACAACUU GAAAUAAGGU UGGCUCAACG GCGCGUGACA GACAAUUCGC GCU GGAACU GCAGUCGGAC CU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21263
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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