8QSV | pdb_00008qsv

Crystal structure of SPOUT1/CENP-32 bound to SAM

PDB DOI: https://doi.org/10.2210/pdb8QSV/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-11 Released: 2024-10-23
Deposition Author(s): Jeyaprakash, A.A., Abad, M.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.280 (Depositor), 0.276 (DCC)
R-Value Work:
0.203 (Depositor), 0.208 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS.

Dharmadhikari, A.V., Abad, M.A., Khan, S., Maroofian, R., Sands, T.T., Ullah, F., Samejima, I., Shen, Y., Wear, M.A., Moore, K.E., Kondakova, E., Mitina, N., Schaub, T., Lee, G.K., Umandap, C.H., Berger, S.M., Iglesias, A.D., Popp, B., Abou Jamra, R., Gabriel, H., Rentas, S., Rippert, A.L., Gray, C., Izumi, K., Conlin, L.K., Koboldt, D.C., Mosher, T.M., Hickey, S.E., Albert, D.V.F., Norwood, H., Lewanda, A.F., Dai, H., Liu, P., Mitani, T., Marafi, D., Eker, H.K., Pehlivan, D., Posey, J.E., Lippa, N.C., Vena, N., Heinzen, E.L., Goldstein, D.B., Mignot, C., de Sainte Agathe, J.M., Al-Sannaa, N.A., Zamani, M., Sadeghian, S., Azizimalamiri, R., Seifia, T., Zaki, M.S., Abdel-Salam, G.M.H., Abdel-Hamid, M.S., Alabdi, L., Alkuraya, F.S., Dawoud, H., Lofty, A., Bauer, P., Zifarelli, G., Afzal, E., Zafar, F., Efthymiou, S., Gossett, D., Towne, M.C., Yeneabat, R., Perez-Duenas, B., Cazurro-Gutierrez, A., Verdura, E., Cantarin-Extremera, V., Marques, A.D.V., Helwak, A., Tollervey, D., Wontakal, S.N., Aggarwal, V.S., Rosenfeld, J.A., Tarabykin, V., Ohta, S., Lupski, J.R., Houlden, H., Earnshaw, W.C., Davis, E.E., Jeyaprakash, A.A., Liao, J.

(2025) Nat Commun 16: 1703-1703

PubMed: 39962046 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-56876-w
Primary Citation of Related Structures:
8QSU, 8QSV, 8QSW

PubMed Abstract:
SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

Organizational Affiliation

Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.

Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.

Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.

Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA.

Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.

Human Molecular Genetics Lab, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.

Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.

Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, WC1N 3BG, London, UK.

Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.

Translational Research Center for the Nervous System, Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China.

Faculty of Life and Health sciences, Shenzhen University of Advanced Technology, 518055, Shenzhen, Guangdong, China.

Department of Pediatrics, Chinese PLA General Hospital, Medical School of Chinese People's Liberation Army, 100853, Beijing, China.

Department of Pediatrics, Fujian Medical University Union Hospital, 350001, Fuzhou, China.

Edinburgh Protein Production Facility (EPPF), University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.

Institute of Neuroscience, Laboratory of Genetics of Brain Development, National Research Lobachevsky State University of Nizhny Novgorod, 603022, 23 Gagarin avenue, Nizhny, Novgorod, Russia.

Institute of Cell and Neurobiology, Charité Universitätsmedizin Berlin, 10117, Berlin, Charitéplatz 1, Germany.

Personalized Care (PCARE) Program, Department of Pathology and Laboratory Medicine; The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.

Medical Genetics, DMG Children's Rehabilitative Services, Phoenix, AZ, 85013, USA.

Division of Clinical Genetics, Department of Pediatrics, Columbia University, Vagelos College of Physicians and Surgeons, New York, NY, USA.

Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.

Praxisfür Humangenetik Tübingen, Tübingen, Germany.

Department of Pathology, Duke University School of Medicine, Durham, NC, USA.

Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.

Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.

Ambry Genetics, Aliso Viejo, CA, USA.

Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, OH, USA.

Division of Neurology, Nationwide Children's Hospital, Columbus, OH 43205, OH, USA.

GeneDx, LLC., Gaithersburg, MD, USA.

Rare Disease Institute, Children's National Hospital, Washington, DC, USA.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

Baylor Genetics, Houston, TX, USA.

Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait.

Department of Medical Genetics, Konya City Hospital, Konya, Turkey.

Texas Children's Hospital, Houston, TX, USA.

Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.

Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.

Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.

Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Département de Génétique, APHP Sorbonne Université, 75013, Paris, France.

Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France.

Pediatric Services, John Hopkins Aramco Health Care, Dhahran, Saudi Arabia.

Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran.

Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, 12622, Cairo, Egypt.

Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, 12622, Cairo, Egypt.

Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

Pediatrics Department, Faculty of Medicine, Tanta University, El-Geesh Street, Tanta, 31527, Egypt.

CENTOGENE GmbH, Am Strande 7, 18055, Rostock, Germany.

Department of Development Pediatrics, The Children's Hospital and The Institute of Child Health, Multan, Pakistan.

Texas Child Neurology, Plano, TX, 75024, USA.

Neurology Consultants of Dallas, Dallas, TX, 75243, USA.

Departments of Pathology and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.

Department of Paediatric Neurology, Hospital Vall d'Hebron, Barcelona, Spain.

Vall d'Hebron Research Institute, Barcelona, Spain.

Department of Paediatrics, Universitat Autònoma de Barcelona, Barcelona, Spain.

Molecular Biology CORE, Biomedical Diagnostic Center (CDB), Hospital, l Clínic de Barcelona, Barcelona, Spain.

Department of Paediatric Neurology, Hospital Infantil Niño Jesús, Madrid, Spain.

Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER (GCV23/ER/3)), ISCIII, Madrid, Spain.

Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität, Munich, Germany.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Institute for Genetic Medicine Pathophysiology, Hokkaido University, Sapporo, Japan.

Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.

Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA. eridavis@luriechildrens.org.

Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA. eridavis@luriechildrens.org.

Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom. jeyaprakash.arulanandam@ed.ac.uk.

Molecular Biology CORE, Biomedical Diagnostic Center (CDB), Hospital, l Clínic de Barcelona, Barcelona, Spain. jeyaprakash.arulanandam@ed.ac.uk.

Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. jl5098@cumc.columbia.edu.

Macromolecule Content

Total Structure Weight: 34.18 kDa
Atom Count: 2,180
Modeled Residue Count: 282
Deposited Residue Count: 307
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase C9orf114	A	307	Homo sapiens	Mutation(s): 0 Gene Names: SPOUT1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T280 (Homo sapiens) Explore Q5T280 Go to UniProtKB: Q5T280
PHAROS: Q5T280 GTEx: ENSG00000198917
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5T280
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]