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- EMDB-23947: Bartonella henselae NrnC complexed with pAAAGG in the presence of... -

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Basic information

Entry
Database: EMDB / ID: EMD-23947
TitleBartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. D4 Symmetry.
Map data
Sample
  • Complex: NrnC octamer complexed with pAAAGG
    • Complex: NrnC octamer
      • Protein or peptide: NanoRNase C
    • Complex: pAAAGG
      • RNA: RNA (5'-R(P*AP*AP*AP*GP*G)-3')
KeywordsRNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesBartonella henselae (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLormand JD / Brownfield B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 United States
CitationJournal: Elife / Year: 2021
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
DepositionMay 5, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0697
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0697
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mqh
  • Surface level: 0.0697
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23947.png

Downloads & links

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Map

FileDownload / File: emd_23947.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 140 pix.
= 173.6 Å		1.24 Å/pix.
x 140 pix.
= 173.6 Å		1.24 Å/pix.
x 140 pix.
= 173.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0697 / Movie #1: 0.0697
Minimum - Maximum-0.13883406 - 0.26841447
Average (Standard dev.)0.0021281694 (±0.014770231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 173.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z173.600173.600173.600
α/β/γ90.00090.00090.000
start NX/NY/NZ7371100
NX/NY/NZ11585169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.1390.2680.002

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Supplemental data

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Additional map: #1

Fileemd_23947_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23947_half_map_1.map
Projections & Slices
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Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_23947_half_map_2.map
Projections & Slices
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Sample components

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Entire : NrnC octamer complexed with pAAAGG

EntireName: NrnC octamer complexed with pAAAGG
Components
  • Complex: NrnC octamer complexed with pAAAGG
    • Complex: NrnC octamer
      • Protein or peptide: NanoRNase C
    • Complex: pAAAGG
      • RNA: RNA (5'-R(P*AP*AP*AP*GP*G)-3')

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Supramolecule #1: NrnC octamer complexed with pAAAGG

SupramoleculeName: NrnC octamer complexed with pAAAGG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 186.621 kDa/nm

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Supramolecule #2: NrnC octamer

SupramoleculeName: NrnC octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bartonella henselae (bacteria)

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Supramolecule #3: pAAAGG

SupramoleculeName: pAAAGG / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bartonella henselae (bacteria) / Synthetically produced: Yes

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Macromolecule #1: NanoRNase C

MacromoleculeName: NanoRNase C / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bartonella henselae (bacteria)
Molecular weightTheoretical: 23.446725 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: RNA (5'-R(P*AP*AP*AP*GP*G)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*GP*G)-3') / type: rna / ID: 2 / Number of copies: 8
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.633072 KDa
SequenceString:
AAAGG

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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: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
25.0 mMC4H11NO3Tris
0.01 %H(C2H4O)nO(C6H4)C9H19NP-40
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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 reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52057
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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