PDBe 5t6r

Electron Microscopy
4.5Å resolution

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
Entry contents:
42 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (45 distinct):
Ribosomal Protein uL1 Chain: S
Molecule details ›
Chain: S
Length: 210 amino acids
Theoretical weight: 17.89 KDa
Source organism: Saccharomyces cerevisiae S288C
60S ribosomal protein L3 Chain: E
Molecule details ›
Chain: E
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
60S ribosomal protein L5 Chain: G
Molecule details ›
Chain: G
Length: 297 amino acids
Theoretical weight: 33.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26321 (Residues: 1-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
60S ribosomal protein L10 Chain: L
Molecule details ›
Chain: L
Length: 221 amino acids
Theoretical weight: 25.41 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P41805 (Residues: 1-221; Coverage: 100%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
60S ribosomal protein L25 Chain: k
Molecule details ›
Chain: k
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
Sequence domains:
60S ribosomal protein L28 Chain: n
Molecule details ›
Chain: n
Length: 149 amino acids
Theoretical weight: 16.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P02406 (Residues: 1-149; Coverage: 100%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
60S ribosomal protein L29 Chain: o
Molecule details ›
Chain: o
Length: 59 amino acids
Theoretical weight: 6.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05747 (Residues: 1-59; Coverage: 100%)
Gene names: RPL29, YFR032BW, YFR032C-A, YL43
Sequence domains: Ribosomal L29e protein family
60S ribosomal protein L30 Chain: p
Molecule details ›
Chain: p
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L32 Chain: r
Molecule details ›
Chain: r
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
60S ribosomal protein L38 Chain: x
Molecule details ›
Chain: x
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39 Chain: y
Molecule details ›
Chain: y
Length: 51 amino acids
Theoretical weight: 6.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04650 (Residues: 1-51; Coverage: 100%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
60S ribosomal protein L2-A Chain: D
Molecule details ›
Chain: D
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX45 (Residues: 1-254; Coverage: 100%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
60S ribosomal protein L4-A Chain: F
Molecule details ›
Chain: F
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
60S ribosomal protein L6-A Chain: H
Molecule details ›
Chain: H
Length: 176 amino acids
Theoretical weight: 20 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 100%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
60S ribosomal protein L7-A Chain: I
Molecule details ›
Chain: I
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
60S ribosomal protein L8-A Chain: J
Molecule details ›
Chain: J
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L9-A Chain: K
Molecule details ›
Chain: K
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
60S ribosomal protein L11-A Chain: M
Molecule details ›
Chain: M
Length: 174 amino acids
Theoretical weight: 19.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0W9 (Residues: 1-174; Coverage: 100%)
Gene names: P8283.14, RP39A, RPL11A, RPL16A, YPR102C
Sequence domains:
60S ribosomal protein L13-A Chain: N
Molecule details ›
Chain: N
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12690 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
60S ribosomal protein L14-A Chain: O
Molecule details ›
Chain: O
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains: Ribosomal protein L14
60S ribosomal protein L15-A Chain: a
Molecule details ›
Chain: a
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
60S ribosomal protein L16-A Chain: b
Molecule details ›
Chain: b
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
60S ribosomal protein L17-A Chain: c
Molecule details ›
Chain: c
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05740 (Residues: 1-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
60S ribosomal protein L18-A Chain: d
Molecule details ›
Chain: d
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
60S ribosomal protein L19-A Chain: e
Molecule details ›
Chain: e
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX82 (Residues: 1-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L20-A Chain: f
Molecule details ›
Chain: f
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S ribosomal protein L21-A Chain: g
Molecule details ›
Chain: g
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02753 (Residues: 1-160; Coverage: 100%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L22-A Chain: h
Molecule details ›
Chain: h
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23-A Chain: i
Molecule details ›
Chain: i
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
60S ribosomal protein L24-A Chain: j
Molecule details ›
Chain: j
Length: 155 amino acids
Theoretical weight: 17.66 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04449 (Residues: 1-155; Coverage: 100%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
60S ribosomal protein L26-A Chain: l
Molecule details ›
Chain: l
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
60S ribosomal protein L27-A Chain: m
Molecule details ›
Chain: m
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
60S ribosomal protein L31-A Chain: q
Molecule details ›
Chain: q
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L33-A Chain: s
Molecule details ›
Chain: s
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
60S ribosomal protein L34-A Chain: t
Molecule details ›
Chain: t
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
60S ribosomal protein L35-A Chain: u
Molecule details ›
Chain: u
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
60S ribosomal protein L36-A Chain: v
Molecule details ›
Chain: v
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
60S ribosomal protein L37-A Chain: w
Molecule details ›
Chain: w
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L42-A Chain: Q
Molecule details ›
Chain: Q
Length: 106 amino acids
Theoretical weight: 12.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX27 (Residues: 1-106; Coverage: 100%)
Gene names: N1722, RPL41A, RPL42A, SCL41A, YNL162W
Sequence domains: Ribosomal protein L44
60S ribosomal protein L43-A Chain: R
Molecule details ›
Chain: R
Length: 92 amino acids
Theoretical weight: 10.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX25 (Residues: 1-92; Coverage: 100%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Ubiquitin-60S ribosomal protein L40 Chain: z
Molecule details ›
Chain: z
Length: 128 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CH08 (Residues: 1-128; Coverage: 100%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains:
Sugar ABC transporter substrate-binding protein; 60S ribosomal export protein NMD3 Chain: V
Molecule details ›
Chain: V
Length: 917 amino acids
Theoretical weight: 103.32 KDa
Source organisms: UniProt:
  • Canonical: P38861 (Residues: 2-518; Coverage: 100%)
  • Canonical: A0A0F8NYV9 (Residues: 1-383; Coverage: 92%)
  • nullnull
Gene names: DU74_04045, NMD3, YHR170W, malE
Sequence domains:
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
25S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
5.8S ribosomal RNA Chain: C
Molecule details ›
Chain: C
Length: 158 nucleotides
Theoretical weight: 50.68 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-8368