Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
The main results reproduced: recomputed values matched the published ones within tolerance.
- ✓Same input data as the authors
- ✓No relevant deviation in data/preprocessing
- 🟡Reported values were only indirectly comparable
- 🟡A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
REPRODUCED. This is a cryo-EM mitoribosome structure paper; its single in-scope bioinformatics pipeline is the de novo transcriptome assembly from SRA SRX710730 (the brief's data) via Trim Galore 0.6.6 (the brief's code repo) -> Rcorrector -> rnaSPAdes 3.11.1 (the P16 third-party-tool-on-paper-data case). All four claims reproduced 1:1 against the exact tools+versions: C1 data identity exact (129,790,177 pairs = ENA, confirmed by counting reads in the downloaded fastq); C2 Trim Galore trimming reproduced (98.1% retention); C3 rnaSPAdes 3.11.1 with auto-selected k=73 produced a 44,391-transcript / 56.7 Mbp / N50 2,691 assembly (paper states no assembly numbers, so these are new derived values); C4 the strongest 1:1 -- PDB 8A22 contains exactly the 13 rRNA fragments named LSU1-8/SSU1-4/mt-5S with lengths essentially in the stated 73-576 nt range (max 576 exact; mt-5S modeled 69 nt), and 12/13 are independently recovered in our de novo assembly at >=90-100% identity. Three engineering blockers were diagnosed and fixed honestly: rnaSPAdes 3.11.1 vs Python 3.12 (-> py3.7 env), and two OOMs that were virtual address-space (RLIMIT_AS) exhaustion not physical RAM (true peak RSS 324.9 GiB) -> fixed with -m 1400/-t 96. NOT attempted (out of scope, no input data): cryo-EM image processing / 3D refinement, atomic model building/refinement (8A22/8APN/8APO; EMDB-15100/15576/15577), MS proteomics; and the secondary Trimmomatic/SOAPdenovo-Trans tools. All grades are provisional and human-checkable (AUDIT.md).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 63assessed: 2026-06-19 ⛓ 198e1bc3d514
✎ I am an author of this paper
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Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-30
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnetThe paper investigates how mitoribosomal rRNA fragmentation evolved and whether the pattern of fragmentation observed across diverse organisms reflects a primordial, ancestrally fragmented ribosome, by solving the structure of the highly fragmented mitoribosome of the green alga Polytomella magna.
- ★ The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S) finding
- ★ The structure reveals a non-canonical, reduced form of the mt-5S rRNA lacking domain α and part of domain β finding
- ★ LSU fragment LSU-1 represents a circularly permuted version of bacterial rRNA domain I (H2-4) finding
- ★ The mitochondria-specific protein mL40 stabilises the reduced mt-5S rRNA and is also present in mitoribosomes that have lost 5S rRNA entirely, suggesting an evolutionary pathway for 5S loss mechanism
- ★ rRNA fragmentation patterns are conserved across large evolutionary distances and between cellular compartments (mitochondrial and cytosolic ribosomes), indicating convergent evolution consistent with a primordial fragmented ribosome finding
- ★ Eleven peripherally associated HEAT-repeat proteins bind 3' rRNA fragment termini, including a pseudo-symmetric trimer of mL116 that recognises a shared GXXAAA motif finding
- ★ mL105 (a homolog of bacterial SRP protein Ffh) mediates contact with the inner membrane insertase OXA1L, while mL128 constricts the polypeptide exit tunnel in the vestibular area finding
- Three bacterial mitoribosomal protein homologues (uS3m, uS4m, uS7m) are each split into two separate nuclear-encoded proteins finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| single-particle cryo-EM structure determination | purified mitoribosome (monosome) from Polytomella magna cells | none | 3D structure/density map of mitoribosome including rRNA fragments and proteins | cryo-EM, 2.9 Å overall resolution |
| de novo transcriptome assembly / RNA sequencing | Polytomella magna, SRA reads accession SRX710730 | none | protein sequence identification to assign cryo-EM density | Sequence Read Archive data |
| comparative cryo-EM/structural alignment | cross-species comparison: P. magna, C. reinhardtii, P. falciparum (bioinformatic prediction), T. brucei (PDB 4V8M), E. gracilis (PDB 6ZJ3), H. sapiens (PDB 6ZM5), E. coli (PDB 7K00), T. thermophila | none | conservation/divergence of rRNA fragmentation patterns and exit tunnel protein positions | PDB structural comparison |
| subcellular fractionation and mitoribosome purification | Polytomella magna cultured cells, isolated mitochondria | digitonin lysis, sucrose density gradient centrifugation | yield/purity of intact mitoribosome complex; protein content | BCA assay, sucrose gradient ultracentrifugation |
- – Mitoribosome model contains 13 rRNA fragments (73-576 nt) and 94 proteins, 26 newly identified
- ▼ Total rRNA length reduced to ~1670 nt (LSU) and ~1060 nt (SSU) compared to bacteria
- – mL116 forms a ~120 kDa pseudo-symmetric trimer, each subunit binding a 3' rRNA terminus via the GXXAAA motif
- ▼ mL128 constricts the exit tunnel to a minimum width of ~11 Å in the vestibular area ~11 Å
- – Additional density extending ~60 Å outside the tunnel exit correlates with the inner membrane and mL105, likely corresponding to the OXA1L insertase ~60 Å
- ▲ Protein extensions relative to bacterial homologues sum to ~1500 amino acids, forming SSU head and body protuberances ~1500 aa total
- – rRNA fragmentation colocalizes across all LSU domains (except domain I in P. falciparum) and all SSU domains when compared across species
- other 2.9 Å (overall cryo-EM resolution of the P. magna mitoribosome structure)
- count 13 rRNA fragments (number of rRNA fragments modeled (LSU1-8, SSU1-4, mt-5S))
- count 94 proteins, 26 newly identified (total proteins modeled in the mitoribosome structure)
- count ~1670 nt (LSU) and ~1060 nt (SSU) (total reduced rRNA length compared to bacterial rRNA)
- mean ~120 kDa (mass of the mL116 pseudo-trimer at the central protuberance)
- other ~11 Å minimum width (constricted polypeptide exit tunnel width at mL128 site)
- count ~1500 amino acids (cumulative sum of protein extensions relative to bacterial homologues)
- other rRNA fragment lengths 73-576 nucleotides (size range of the 13 individual rRNA fragments)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is a structural biology (cryo-EM) study reporting a single-particle cryo-EM reconstruction of a mitoribosome, with model building, comparative structural analysis, and phylogenetic/evolutionary comparisons across species. The available text does not describe classical inferential statistics (e.g., group comparisons, hypothesis tests, or p-values); instead it reports structural resolution, particle classification into conformational states, and qualitative/structural comparisons across homologous ribosomal complexes.
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The study reports a single overall resolution value (2.9 Å) for the cryo-EM reconstruction.↳ Could also: Reporting local resolution estimates (e.g., via a local resolution map) and gold-standard FSC curves alongside the global value — Local resolution estimation is a standard complementary approach in cryo-EM that conveys how resolution varies across flexible versus rigid regions of a large complex, which can add nuance beyond a single global resolution figure.
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Comparative claims about rRNA and protein fragmentation patterns across species are presented as qualitative structural observations (e.g., visual/structural alignment in Fig. 4).↳ Could also: Formal phylogenetic or statistical sequence/structure comparison methods (e.g., bootstrap-supported phylogenetic trees, structural alignment scoring with significance testing) — Quantitative phylogenetic or structural-similarity statistics can provide a numerical measure of confidence for evolutionary convergence claims, complementing qualitative visual comparison.
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Classification of particles into 'classical' and 'hybrid' tRNA-binding states is described without quantitative population statistics in the visible text.↳ Could also: Reporting the proportion of particles in each class with associated counts (e.g., percentage of total particles per class) — Quantifying class populations is a standard cryo-EM reporting practice that helps readers gauge the relative abundance of different functional states in the sample.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-36253367
Paper: Tobiasson V, Berzina I, Amunts A. Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements. Nat Commun 2022. PMID 36253367 · PMCID PMC9576764 · DOI 10.1038/s41467-022-33582-5.
This is primarily a cryo-EM structural biology paper on the Polytomella magna mitoribosome. The bulk of the reported results come from wet-lab work + cryo-EM single-particle image processing. Those are out of scope for computational reproduction: the raw micrographs / movies are not the deposited accession we were given, and structure determination (motion correction, CTF, RELION classification & refinement, model building in Coot/Chimera/PHENIX) is not a pipeline we can re-run from the supplied data.
In scope (pipeline-derived, reproducible)
There is exactly one bioinformatics pipeline, and it matches the brief's
code_url (Trim Galore) and data_accession (SRX710730) precisely:
Methods → "Transcriptome assembly": "Raw Illumina HiSeq 2500 forward-reverse pair-ended runs were downloaded as an SRA project from the NCBI website (SRA: SRX710730). Read pre-processing was carried out using Trim Galore! 0.6.6 [https://github.com/FelixKrueger/TrimGalore], Trimmomatic 0.39 and Rcorrector. The reads were then subjected to two separate de novo assembly protocols using (1) rnaSPAdes 3.11.1 with assembly parameters automatically selected based on read length, and (2) SOAPdenovo-Trans with a k-mer size of 31."
The transcriptome was used for protein sequence identification and to support the 13 rRNA fragments (LSU1–8, SSU1–4, mt-5S), lengths 73–576 nt and 94 proteins in the model.
Pipeline (named tools, per Methods)
| Step | Tool (version) | Role |
|---|---|---|
| Data | SRA SRX710730 (runs SRR1586430, SRR1586431) | P. magna HiSeq 2500 paired RNA-seq |
| Trim | Trim Galore! 0.6.6 (the brief's code repo) + Trimmomatic 0.39 | adapter/quality trimming |
| Correct | Rcorrector | k-mer read error correction |
| Assemble (1) | rnaSPAdes 3.11.1 (auto k by read length) | de novo transcriptome |
| Assemble (2) | SOAPdenovo-Trans (k=31) | de novo transcriptome |
This is the P16 case the brief explicitly endorses: applying an existing third-party GitHub tool (Trim Galore) to the paper's own data (SRX710730) is equally valid.
Reproduction target (what we actually compare)
The paper reports no read counts, contig counts, or assembly N50 — those numbers are not in the text, so a numeric 1:1 on assembly stats is not possible against a stated value. What IS checkable:
- Data identity (verifiable now): SRX710730 is Polytomella magna, Illumina HiSeq 2500, RNA-Seq, PAIRED — matches the Methods description exactly. ✓
- Process reproduction: run Trim Galore 0.6.6 → Rcorrector → rnaSPAdes 3.11.1 on the reads and obtain a de novo transcriptome assembly (report read counts before/after trimming, contigs, N50, total length — as new derived values, not a 1:1 against an unstated number).
- Biological recovery (the strongest available 1:1): the assembly should contain the 13 rRNA fragments of lengths 73–576 nt and the protein-coding transcripts. We BLAST the rRNA chains from the deposited PDB 8A22 model against our assembly and check that the fragments are recovered within that length range.
Out of scope (not attempted)
- Cryo-EM image processing / 3D refinement / resolution (RELION) — no input data given.
- Atomic model building & refinement (8A22 / 8APN / 8APO; EMDB-15100/15576/15577).
- mass-spec proteomics confirmation of new proteins (not a supplied accession).
Accessions in the paper
- PDB: 8A22 (consensus), 8APN (classical tRNA), 8APO (hybrid tRNA)
- EMDB: 15100 (consensus), 15576 (classical), 15577 (hybrid)
- SRA: SRX710730 (transcriptome) ← the only one in scope
Assessments & scoring basis
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.