Evidence map›Paper›PMID 40246839›Full record

ArticleNature communications2025

Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.

Koki Nakamura, Saeko Aoyama-Ishiwatari, Takahiro Nagao, Mohammadreza Paaran, Christopher J Obara, Yui Sakurai-Saito, Jake Johnston, Yudan Du, Shogo Suga, Masafumi Tsuboi and 13 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.

0numbers the graph read from it
0cells of the map it votes in
34citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

34 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors.

Koki Nakamura *Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.ORCID http://orcid.org/0000-0003-4885-4526
Saeko Aoyama-Ishiwatari *Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.ORCID http://orcid.org/0009-0001-6439-8922
Takahiro Nagao *Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Mohammadreza PaaranSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10028, USA.ORCID http://orcid.org/0000-0002-8402-0134
Christopher J ObaraJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.
Yui Sakurai-SaitoDepartment of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Jake JohnstonSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10028, USA.
Yudan DuDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Shogo SugaDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Masafumi TsuboiDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Makoto NakakidoDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Kouhei TsumotoDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.ORCID http://orcid.org/0000-0001-7643-5164
Yusuke KishiGraduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.ORCID http://orcid.org/0000-0003-2846-5400
Yukiko GotohGraduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.ORCID http://orcid.org/0000-0001-9367-6648
Chulhwan KwakDepartment of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
Hyun-Woo RheeSchool of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.ORCID http://orcid.org/0000-0002-3817-3455
Jeong Kon SeoGraduate School of Semiconductor Materials and Devices Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Hidetaka KosakoDivision of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan.ORCID http://orcid.org/0000-0003-3228-6368
Clint PotterSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10028, USA.
Bridget CarragherSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10028, USA.ORCID http://orcid.org/0000-0002-0624-5020
Jennifer Lippincott-SchwartzJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.ORCID http://orcid.org/0000-0002-8601-3501
Franck PolleuxDepartment of Neuroscience, Columbia University Medical Center, New York, NY, 10032, USA.ORCID http://orcid.org/0000-0003-4313-0481
Yusuke HirabayashiDepartment of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan. hirabayashi@chembio.t.u-tokyo.ac.jp.ORCID http://orcid.org/0000-0003-3950-6781

Funding

Development, Maintenance, and Human-Specific Evolution of Cortical CircuitsR35NS127232 · NINDS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI FRANCK POLLEUX · 2022 to 2026
$6.1M
Japan Agency for Medical Research and Development (AMED) JP19dm0207082Japan Agency for Medical Research and Development (AMED) JP21wm0525015MEXT | Japan Society for the Promotion of Science (JSPS) JP20H04898MEXT | Japan Society for the Promotion of Science (JSPS) JP22H05532MEXT | Japan Society for the Promotion of Science (JSPS) JP24H01269MEXT | Japan Society for the Promotion of Science (JSPS) JP24H01348NINDS NIH HHS R35 NS127232Secom Science and Technology Foundation (SSTF) N/AUehara Memorial Foundation N/A
6 · The paper itself

Abstract

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identify the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-electron tomography, and correlative light-electron microscopy. Single molecule tracking reveals highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and captures at MERCS. Overexpression of FKBP8 is sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrate their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

Indexed as

Endoplasmic ReticulumMitochondriaMitochondrial MembranesTacrolimus Binding ProteinsAnimalsCRISPR-Cas SystemsCryoelectron MicroscopyHEK293 CellsHeLa CellsHumansMembrane ProteinsProteomicsFKBP8 protein, humanMembrane ProteinsTacrolimus Binding Proteins

Identifiers

PMID40246839
PMCPMC12006300

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.