› 8eup

Electron Microscopy
3.1Å resolution

Ytm1 associated 60S nascent ribosome State 1A

Released:
DOI: 10.2210/pdb8eup/pdb
PDB entry 8eup coloured by chain, front view.
PDB entry 8eup coloured by chain, side view.
PDB entry 8eup coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
Chromatin localization of nucleophosmin organizes ribosome biogenesis.
Ugolini I, Bilokapic S, Ferrolino M, Teague J, Yan Y, Zhou X, Deshmukh A, White M, Kriwacki RW, Halic M
Mol Cell (2022)
PMID: 36423630
Related structures: EMD-24410

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 40-mer (preferred)
PDBe Complex ID:
PDB-CPX-221168 (preferred)
Entry contents:
37 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (40 distinct):
Protein mak16 Chain: 3
Molecule details ›
Chain: 3
Length: 302 amino acids
Theoretical weight: 35.69 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UTE6 (Residues: 1-302; Coverage: 100%)
Gene names: SPAC222.06, mak16
Sequence domains:
Ribosomal RNA-processing protein 1 homolog Chain: 4
Molecule details ›
Chain: 4
Length: 217 amino acids
Theoretical weight: 25.78 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9Y7M6 (Residues: 1-217; Coverage: 100%)
Gene name: SPBC9B6.07
Sequence domains: Nucleolar protein,Nop52
Ribosome biogenesis protein nsa1 Chain: 5
Molecule details ›
Chain: 5
Length: 387 amino acids
Theoretical weight: 43.83 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94698 (Residues: 1-387; Coverage: 100%)
Gene names: SPBC83.15, nsa1
Ribosome biogenesis protein brx1 Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 33.95 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9HGL6 (Residues: 1-295; Coverage: 100%)
Gene names: SPBC800.06, brx1
Sequence domains: Brix domain
Large ribosomal subunit protein uL3A Chain: B
Molecule details ›
Chain: B
Length: 388 amino acids
Theoretical weight: 43.89 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P40372 (Residues: 1-388; Coverage: 100%)
Gene names: SPAC17A5.03, rpl301, rpl3a
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4B Chain: C
Molecule details ›
Chain: C
Length: 363 amino acids
Theoretical weight: 39.98 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P784 (Residues: 1-363; Coverage: 100%)
Gene names: SPBC1711.06, rpl401, rpl4b
Sequence domains:
ATP-dependent RNA helicase has1 Chain: D
Molecule details ›
Chain: D
Length: 578 amino acids
Theoretical weight: 65.36 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q09916 (Residues: 1-578; Coverage: 100%)
Gene names: SPAC1F7.02c, has1
Sequence domains:
Large ribosomal subunit protein eL6 Chain: E
Molecule details ›
Chain: E
Length: 195 amino acids
Theoretical weight: 21.29 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P79071 (Residues: 1-195; Coverage: 100%)
Gene names: SPCC622.18, rpl6
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30B Chain: F
Molecule details ›
Chain: F
Length: 250 amino acids
Theoretical weight: 28.5 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P25457 (Residues: 1-250; Coverage: 100%)
Gene names: SPAC3H5.07, rpl702, rpl7b
Sequence domains:
Large ribosomal subunit protein eL8 Chain: G
Molecule details ›
Chain: G
Length: 259 amino acids
Theoretical weight: 28.66 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O13672 (Residues: 1-259; Coverage: 100%)
Gene names: SPBC29A3.04, rpl8
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chain: H
Molecule details ›
Chain: H
Length: 190 amino acids
Theoretical weight: 21.54 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10232 (Residues: 1-190; Coverage: 100%)
Gene names: SPAC4G9.16c, rpl901, rpl9a
Sequence domains: Ribosomal protein L6
Probable rRNA-processing protein ebp2 Chain: J
Molecule details ›
Chain: J
Length: 333 amino acids
Theoretical weight: 37.89 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O13802 (Residues: 1-333; Coverage: 100%)
Gene names: SPAC17H9.05, ebp2
Sequence domains: Eukaryotic rRNA processing protein EBP2
Putative ribosome biogenesis protein C8F11.04 Chain: K
Molecule details ›
Chain: K
Length: 373 amino acids
Theoretical weight: 41.43 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UT32 (Residues: 1-373; Coverage: 100%)
Gene name: SPAC8F11.04
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein eL13 Chain: L
Molecule details ›
Chain: L
Length: 208 amino acids
Theoretical weight: 23.58 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74175 (Residues: 1-208; Coverage: 100%)
Gene names: SPAC664.05, rpl13
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 Chain: M
Molecule details ›
Chain: M
Length: 134 amino acids
Theoretical weight: 15.24 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94238 (Residues: 1-134; Coverage: 100%)
Gene names: SPAC1805.13, rpl14
Sequence domains:
Large ribosomal subunit protein eL15A Chain: N
Molecule details ›
Chain: N
Length: 201 amino acids
Theoretical weight: 23.86 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74895 (Residues: 1-201; Coverage: 100%)
Gene names: SPCC576.11, rpl15, rpl1501, rpl15a
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13B Chain: O
Molecule details ›
Chain: O
Length: 197 amino acids
Theoretical weight: 22.22 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O42991 (Residues: 1-197; Coverage: 100%)
Gene names: SPBC24E9.13c, SPBC839.13c, rpl1601, rpl16b
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: P
Molecule details ›
Chain: P
Length: 187 amino acids
Theoretical weight: 20.85 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14339 (Residues: 1-187; Coverage: 100%)
Gene names: SPBC2F12.04, rpl17, rpl1701, rpl17a
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: Q
Molecule details ›
Chain: Q
Length: 187 amino acids
Theoretical weight: 21.24 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10192 (Residues: 1-187; Coverage: 100%)
Gene names: SPBC11C11.07, rpl18, rpl1801, rpl18a
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL20A Chain: S
Molecule details ›
Chain: S
Length: 176 amino acids
Theoretical weight: 20.64 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P0CT68 (Residues: 1-176; Coverage: 100%)
Gene names: SPAC3A12.10, rpl2001, rpl20a
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein uL14A Chain: V
Molecule details ›
Chain: V
Length: 139 amino acids
Theoretical weight: 14.91 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P0CT60 (Residues: 1-139; Coverage: 100%)
Gene names: SPAC3G9.03, rpl23, rpl2301, rpl23a
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 126 amino acids
Theoretical weight: 14.38 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P78946 (Residues: 1-126; Coverage: 100%)
Gene names: SPBC29B5.03c, rpl26
Sequence domains:
Probable nucleolar GTP-binding protein 1 Chain: b
Molecule details ›
Chain: b
Length: 642 amino acids
Theoretical weight: 72.92 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94659 (Residues: 1-642; Coverage: 100%)
Gene names: SPBC651.01c, SPBC725.18c, nog1
Sequence domains:
Large ribosomal subunit protein eL32A Chain: e
Molecule details ›
Chain: e
Length: 127 amino acids
Theoretical weight: 14.49 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P79015 (Residues: 1-127; Coverage: 100%)
Gene names: SPAC3H5.10, rpl3202, rpl32a
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33B Chain: f
Molecule details ›
Chain: f
Length: 108 amino acids
Theoretical weight: 12.13 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9USG6 (Residues: 1-108; Coverage: 100%)
Gene names: SPCP31B10.08c, rpl33b, rpl35a, rpl37
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein uL29 Chain: h
Molecule details ›
Chain: h
Length: 122 amino acids
Theoretical weight: 14.33 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74904 (Residues: 1-122; Coverage: 100%)
Gene names: SPCC613.05c, rpl35
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36B Chain: i
Molecule details ›
Chain: i
Length: 99 amino acids
Theoretical weight: 11.29 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94658 (Residues: 1-99; Coverage: 100%)
Gene names: SPBC405.07, rpl3602, rpl36b
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37B Chain: j
Molecule details ›
Chain: j
Length: 91 amino acids
Theoretical weight: 10.11 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P05733 (Residues: 1-91; Coverage: 100%)
Gene names: SPCC1223.05c, rpl3702, rpl37b
Sequence domains: Ribosomal protein L37e
Ribosome biogenesis protein erb1 Chain: m
Molecule details ›
Chain: m
Length: 740 amino acids
Theoretical weight: 83.05 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74399 (Residues: 1-740; Coverage: 100%)
Gene names: SPBC4F6.13c, erb1
Sequence domains:
Uncharacterized RNA-binding protein C1827.05c Chain: o
Molecule details ›
Chain: o
Length: 276 amino acids
Theoretical weight: 31.47 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74978 (Residues: 1-276; Coverage: 100%)
Gene name: SPCC1827.05c
Sequence domains: RNA recognition motif
Ribosome biogenesis protein nsa2 Chain: r
Molecule details ›
Chain: r
Length: 260 amino acids
Theoretical weight: 29.77 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UU79 (Residues: 1-260; Coverage: 100%)
Gene names: SPCP1E11.08, nsa2
Sequence domains: Ribosomal protein S8e
Large ribosomal subunit protein uL30A Chain: t
Molecule details ›
Chain: t
Length: 249 amino acids
Theoretical weight: 29.22 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: P17937 (Residues: 1-249; Coverage: 100%)
Gene names: SPAC664.06, rlp7, rpl7a
Sequence domains:
Ribosome biogenesis protein rlp24 Chain: u
Molecule details ›
Chain: u
Length: 192 amino acids
Theoretical weight: 22.32 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q10353 (Residues: 1-192; Coverage: 100%)
Gene names: SPAC22E12.13c, rlp24, rpl2403
Sequence domains: Ribosomal protein L24e
Nucleolar protein 16 Chain: v
Molecule details ›
Chain: v
Length: 209 amino acids
Theoretical weight: 23.99 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9Y7Z1 (Residues: 1-209; Coverage: 100%)
Gene names: SPBC1539.10, nop16
Sequence domains: Ribosome biogenesis protein Nop16
Brix domain-containing protein C4F8.04 Chain: x
Molecule details ›
Chain: x
Length: 306 amino acids
Theoretical weight: 35.9 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14180 (Residues: 1-306; Coverage: 100%)
Gene name: SPAC4F8.04
Sequence domains: Brix domain
Eukaryotic translation initiation factor 6 Chain: y
Molecule details ›
Chain: y
Length: 244 amino acids
Theoretical weight: 26.25 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94476 (Residues: 1-244; Coverage: 100%)
Gene names: SPCC1919.09, tif6
Sequence domains: eIF-6 family
Large ribosomal subunit protein eL21A Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.42 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UUC1 (Residues: 1-160; Coverage: 100%)
Gene names: SPBC365.03c, rpl21, rpl2101, rpl21a
Sequence domains: Ribosomal protein L21e
RNA (1422-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 3497 nucleotides
Theoretical weight: 1129.52 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
RNA (146-MER) Chain: 2
Molecule details ›
Chain: 2
Length: 165 nucleotides
Theoretical weight: 52.88 KDa
Sequence domains: 5.8S ribosomal RNA
RNA (55-MER) Chain: 6
Molecule details ›
Chain: 6
Length: 300 nucleotides
Theoretical weight: 95.69 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-24410

Quick links

Citations

1 citations in other articles

Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Zhang et al. (2023)

1 mention without citation

Chromatin localization of nucleophosmin organizes ribosome biogenesis.
Ugolini et al. (2022)