[English] 日本語
Yorodumi
- EMDB-35535: Human ornithine transcarbamylase expressed using mRNA lipid nanop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35535
TitleHuman ornithine transcarbamylase expressed using mRNA lipid nanoparticles in human cells and PEGylated
Map dataPrimary map by PostProcess
Sample
  • Complex: Human ornithine transcarbamylase
    • Protein or peptide: Ornithine transcarbamylase
KeywordsMitochondrial protein / Transferase / Trimer
Function / homology
Function and homology information


response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import ...response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import / urea cycle / amino acid binding / midgut development / response to zinc ion / phosphate ion binding / liver development / phospholipid binding / response to insulin / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / identical protein binding
Similarity search - Function
Ornithine/putrescine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
Ornithine transcarbamylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKondo K / Yamazaki K / Kubara K / Ishii S / Suzuki Y / Miyazaki T / Mitsuhashi K / Ito M / Tsukahara K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther Nucleic Acids / Year: 2023
Title: Lipid nanoparticle-targeted mRNA formulation as a treatment for ornithine-transcarbamylase deficiency model mice.
Authors: Kazuto Yamazaki / Kenji Kubara / Satoko Ishii / Keita Kondo / Yuta Suzuki / Takayuki Miyazaki / Kaoru Mitsuhashi / Masashi Ito / Kappei Tsukahara /
Abstract: Ornithine transcarbamylase (OTC) plays a significant role in the urea cycle, a metabolic pathway functioning in the liver to detoxify ammonia. OTC deficiency (OTCD) is the most prevalent urea cycle ...Ornithine transcarbamylase (OTC) plays a significant role in the urea cycle, a metabolic pathway functioning in the liver to detoxify ammonia. OTC deficiency (OTCD) is the most prevalent urea cycle disorder. Here, we show that intravenously delivered human (h) mRNA by lipid nanoparticles (LNP) was an effective treatment for OTCD by restoring the urea cycle. We observed a homotrimer conformation of hOTC proteins produced by the mRNA-LNP in cells by cryo-electron microscopy. The immunohistochemistry revealed the mitochondria localization of produced hOTC proteins in hepatocytes in mice. In livers of mice intravenously injected with h-mRNA/LNP at 1.0 mg/kg, the delivered h mRNA levels steeply decreased with a half-life (t) of 7.1 h, whereas the produced hOTC protein levels retained for 5 days and then declined with a t of 2.2 days. In OTCD model mice (high-protein diet-fed hemizygous males), a single dose of h-mRNA/LNP at 3.0 mg/kg ameliorated hyperammonemia and weight loss with prolonged survival rate (22 days) compared with that of untreated mice (11 days). Weekly repeated doses at 0.3 and 1.0 mg/kg were well tolerated in wild-type mice and showed a dose-dependent amelioration of survival rate in OTCD mice, thus, showing the therapeutic potential of LNP-formulated h mRNA for OTCD.
History
DepositionMar 3, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35535.png

Downloads & links

-
Map

FileDownload / File: emd_35535.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map by PostProcess
Voxel sizeX=Y=Z: 0.841 Å
Density
Contour LevelBy AUTHOR: 0.0026
Minimum - Maximum-0.006914478 - 0.012616531
Average (Standard dev.)0.00007022636 (±0.00058561674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 168.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_35535_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 by Refine3D

Fileemd_35535_half_map_1.map
AnnotationHalf map 1 by Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 by Refine3D

Fileemd_35535_half_map_2.map
AnnotationHalf map 2 by Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human ornithine transcarbamylase

EntireName: Human ornithine transcarbamylase
Components
  • Complex: Human ornithine transcarbamylase
    • Protein or peptide: Ornithine transcarbamylase

-
Supramolecule #1: Human ornithine transcarbamylase

SupramoleculeName: Human ornithine transcarbamylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118 KDa

-
Macromolecule #1: Ornithine transcarbamylase

MacromoleculeName: Ornithine transcarbamylase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ornithine carbamoyltransferase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NKVQLKGRDL LTLKNFTGEE IKYMLWLSAD LKFRIKQKGE YLPLLQGKSL GMIFEKRSTR TRLSTETGFA LLGGHPCFLT TQDIHLGVNE SLTDTARVLS SMADAVLARV YKQSDLDTLA KEASIPIING LSDLYHPIQI LADYLTLQEH YSSLKGLTLS WIGDGNNILH ...String:
NKVQLKGRDL LTLKNFTGEE IKYMLWLSAD LKFRIKQKGE YLPLLQGKSL GMIFEKRSTR TRLSTETGFA LLGGHPCFLT TQDIHLGVNE SLTDTARVLS SMADAVLARV YKQSDLDTLA KEASIPIING LSDLYHPIQI LADYLTLQEH YSSLKGLTLS WIGDGNNILH SIMMSAAKFG MHLQAATPKG YEPDASVTKL AEQYAKENGT KLLLTNDPLE AAHGGNVLIT DTWISMGQEE EKKKRLQAFQ GYQVTMKTAK VAASDWTFLH CLPRKPEEVD DEVFYSPRSL VFPEAENRKW TIMAVMVSLL TDYSPQLQKP KFGGSGGSGG DYKDHDGDYK DHDIDYKDDD K

UniProtKB: Ornithine transcarbamylase, mitochondrial

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloridesodium chloride

Details: 50 mM HEPES-NaOH (pH 7.5), 200 mM NaCl
Sugar embeddingMaterial: amorphous water
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse. PEGylation was introduced to the sample.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Details: An initial model was generated from PDB ID 1C9Y using UCSF ChimeraX 1.4.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 87434
FSC plot (resolution estimation)

+
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