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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23942 | |||||||||
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Title | Bartonella henselae NrnC bound to pGG. C1 reconstruction. | |||||||||
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![]() | RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / 3'-5' exonuclease![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.64 Å | |||||||||
![]() | Lormand JD / Brownfield B | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of NrnC identifies unifying features of dinucleotidases. Authors: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann / ![]() ![]() Abstract: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.2 KB | Display | ![]() |
Images | ![]() | 109.4 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() | 8.6 MB 8.6 MB 8.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mqcMC ![]() 7mplC ![]() 7mpmC ![]() 7mpnC ![]() 7mpoC ![]() 7mppC ![]() 7mpqC ![]() 7mprC ![]() 7mpsC ![]() 7mptC ![]() 7mpuC ![]() 7mqbC ![]() 7mqdC ![]() 7mqeC ![]() 7mqfC ![]() 7mqgC ![]() 7mqhC ![]() 7mqiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_23942_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_23942_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_23942_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NrnC octamer bound to pGG
Entire | Name: NrnC octamer bound to pGG |
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Components |
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-Supramolecule #1: NrnC octamer bound to pGG
Supramolecule | Name: NrnC octamer bound to pGG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 186.621 kDa/nm |
-Supramolecule #2: NrnC octamer
Supramolecule | Name: NrnC octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: pGG
Supramolecule | Name: pGG / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: NanoRNase C
Macromolecule | Name: NanoRNase C / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.446725 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SMTEIRVHQG DLPNLDNYRI DAVAVDTETL GLQPHRDRLC VVQLSSGDGT ADVIQIAKGQ KSAPNLVRLL SDRDITKIFH FGRFDLAIL AHTFGVMPDV VFCTKIASKL TRTYTDRHGL KEICGELLNV NISKQQQSSD WAAETLSRAQ IEYAASDVLY L HRLKDIFE ...String: SMTEIRVHQG DLPNLDNYRI DAVAVDTETL GLQPHRDRLC VVQLSSGDGT ADVIQIAKGQ KSAPNLVRLL SDRDITKIFH FGRFDLAIL AHTFGVMPDV VFCTKIASKL TRTYTDRHGL KEICGELLNV NISKQQQSSD WAAETLSRAQ IEYAASDVLY L HRLKDIFE ERLKREERES VAKACFQFLP MRANLDLLGW SEIDIFAHS UniProtKB: 3'-5' exonuclease |
-Macromolecule #2: RNA (5'-R(P*GP*G)-3')
Macromolecule | Name: RNA (5'-R(P*GP*G)-3') / type: rna / ID: 2 / Number of copies: 8 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 645.454 Da |
Sequence | String: GG |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |