Pseudouridine synthase PUS1 and initiation factor mtIF2 are human mitoribosomal small subunit assembly factors
Singh, V., Shiriaev, D., Bilalli, L., Khawaja, A., Rorbach, J.(2026) Nat Commun 17: 5564
Experimental Data Snapshot
wwPDB Validation 3D Report Full Report
(2026) Nat Commun 17: 5564
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S34, mitochondrial | A [auth 0] | 218 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82930 GTEx:  ENSG00000074071  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82930 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S35, mitochondrial | B [auth 1] | 323 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82673 GTEx:  ENSG00000061794  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82673 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Aurora kinase A-interacting protein | C [auth 3] | 199 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9NWT8 GTEx:  ENSG00000175756  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NWT8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S2, mitochondrial | D [auth B] | 296 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y399 GTEx:  ENSG00000122140  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y399 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S24, mitochondrial | E [auth C] | 167 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
GTEx:  ENSG00000062582  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96EL2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S6, mitochondrial | F [auth E] | 125 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82932 GTEx:  ENSG00000243927  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82932 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S7, mitochondrial | G [auth F] | 242 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y2R9 GTEx:  ENSG00000125445  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y2R9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S10, mitochondrial | 201 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82664 GTEx:  ENSG00000048544  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82664 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S11, mitochondrial | 194 | Homo sapiens | Mutation(s): 1  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82912 GTEx:  ENSG00000181991  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82912 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S12, mitochondrial | 138 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  O15235 GTEx:  ENSG00000128626  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O15235 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S14, mitochondrial | 128 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  O60783 GTEx:  ENSG00000120333  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O60783 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S15, mitochondrial | 257 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82914 GTEx:  ENSG00000116898  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82914 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S16, mitochondrial | 137 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y3D3 GTEx:  ENSG00000182180  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y3D3 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S17, mitochondrial | 130 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y2R5 GTEx:  ENSG00000239789  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y2R5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S18b, mitochondrial | 258 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y676 GTEx:  ENSG00000204568  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y676 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S18c, mitochondrial | 142 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y3D5 GTEx:  ENSG00000163319  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y3D5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS21m | 87 | Homo sapiens | Mutation(s): 1  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82921 GTEx:  ENSG00000266472  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82921 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S22, mitochondrial | 360 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82650 GTEx:  ENSG00000175110  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82650 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S23, mitochondrial | 190 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y3D9 GTEx:  ENSG00000181610  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y3D9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S25, mitochondrial | 173 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82663 GTEx:  ENSG00000131368  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82663 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S26, mitochondrial | 205 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
GTEx:  ENSG00000125901  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9BYN8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 22 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S28, mitochondrial | V [auth W] | 187 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y2Q9 GTEx:  ENSG00000147586  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y2Q9 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 23 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S29, mitochondrial | W [auth X] | 398 | Homo sapiens | Mutation(s): 0  EC: 3.6.5 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P51398 GTEx:  ENSG00000132676  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P51398 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 24 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S31, mitochondrial | X [auth Y] | 395 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q92665 GTEx:  ENSG00000102738  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q92665 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 25 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S33, mitochondrial | Y [auth Z] | 106 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q9Y291 GTEx:  ENSG00000090263  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y291 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 26 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S5, mitochondrial | Z [auth D] | 430 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82675 GTEx:  ENSG00000144029  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82675 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 27 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S9, mitochondrial | AA [auth G] | 396 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  P82933 GTEx:  ENSG00000135972  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P82933 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 28 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 28S ribosomal protein S27, mitochondrial | BA [auth V] | 414 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q92552 GTEx:  ENSG00000113048  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q92552 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 29 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Pentatricopeptide repeat domain-containing protein 3, mitochondrial | CA [auth 4] | 689 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q96EY7 GTEx:  ENSG00000132300  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96EY7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 30 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 12S rRNA N4-methylcytidine (m4C) methyltransferase | DA [auth b] | 407 | Homo sapiens | Mutation(s): 0  EC: 2.1.1 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  A6NJ78 GTEx:  ENSG00000169519  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6NJ78 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 32 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative ribosome-binding factor A, mitochondrial | FA [auth a] | 343 | Homo sapiens | Mutation(s): 0  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS:  Q8N0V3 GTEx:  ENSG00000101546  | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8N0V3 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 31 | ||||
| Molecule | Chains | Length | Organism | Image |
|---|---|---|---|---|
| 12S mitochondrial rRNA | EA [auth A] | 954 | Homo sapiens | ![]() |
Sequence AnnotationsExpand | ||||
Reference Sequence | ||||
| Ligands 8 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Download:Ideal Coordinates CCD File | NA [auth A] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N | |||
| ATP Download:Ideal Coordinates CCD File | KA [auth X] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N | |||
| GDP Download:Ideal Coordinates CCD File | LA [auth X] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N | |||
| SPM Download:Ideal Coordinates CCD File | OA [auth A] | SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N | |||
| FES Download:Ideal Coordinates CCD File | IA [auth P], JA [auth T] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N | |||
| ZN Download:Ideal Coordinates CCD File | HA [auth O] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| K Download:Ideal Coordinates CCD File | GA [auth F] TB [auth A] UB [auth A] VB [auth A] WB [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
| MG Download:Ideal Coordinates CCD File | AB [auth A] BB [auth A] CB [auth A] DB [auth A] EB [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.21.1_5286: |
| RECONSTRUCTION | RELION |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Knut and Alice Wallenberg Foundation | Sweden | 023405053 |