› 6hma

Electron Microscopy
2.65Å resolution

Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit

Released:
DOI: 10.2210/pdb6hma/pdb
PDB entry 6hma coloured by chain, front view.
PDB entry 6hma coloured by chain, side view.
PDB entry 6hma coloured by chain, top view.
Source organism: Staphylococcus aureus
Entry authors: Eyal Z, Cimicata G, Matzov D, Fox T, de Val N, Zimmerman E, Bashan A, Yonath A
Related structures: EMD-0243

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 29-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140908 (preferred)
Entry contents:
27 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (29 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 274 amino acids
Theoretical weight: 29.83 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P60430 (Residues: 2-275; Coverage: 99%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 215 amino acids
Theoretical weight: 23.2 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW06 (Residues: 2-216; Coverage: 98%)
Gene names: SAOUHSC_02512, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 206 amino acids
Theoretical weight: 22.36 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW07 (Residues: 2-207; Coverage: 100%)
Gene names: SAOUHSC_02511, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 158 amino acids
Theoretical weight: 17.65 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW18 (Residues: 19-176; Coverage: 88%)
Gene names: SAOUHSC_02500, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 175 amino acids
Theoretical weight: 19.5 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW21 (Residues: 2-176; Coverage: 98%)
Gene names: SAOUHSC_02496, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: H
Molecule details ›
Chain: H
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW38 (Residues: 1-145; Coverage: 100%)
Gene names: SAOUHSC_02478, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW16 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02502, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: J
Molecule details ›
Chain: J
Length: 146 amino acids
Theoretical weight: 15.63 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P0A0F8 (Residues: 1-146; Coverage: 100%)
Gene names: SAOUHSC_02492, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: K
Molecule details ›
Chain: K
Length: 137 amino acids
Theoretical weight: 15.6 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW13 (Residues: 1-137; Coverage: 95%)
Gene names: SAOUHSC_02505, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17 Chain: L
Molecule details ›
Chain: L
Length: 120 amino acids
Theoretical weight: 13.58 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW33 (Residues: 3-122; Coverage: 98%)
Gene names: SAOUHSC_02484, rplQ
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: M
Molecule details ›
Chain: M
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW22 (Residues: 1-119; Coverage: 100%)
Gene names: SAOUHSC_02495, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19 Chain: N
Molecule details ›
Chain: N
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 13.46 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXQ1 (Residues: 2-117; Coverage: 98%)
Gene names: SAOUHSC_01784, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: P
Molecule details ›
Chain: P
Length: 102 amino acids
Theoretical weight: 11.35 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXS8 (Residues: 1-102; Coverage: 100%)
Gene names: SAOUHSC_01757, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: Q
Molecule details ›
Chain: Q
Length: 112 amino acids
Theoretical weight: 12.33 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW11 (Residues: 1-112; Coverage: 96%)
Gene names: SAOUHSC_02507, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: R
Molecule details ›
Chain: R
Length: 89 amino acids
Theoretical weight: 10.38 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW08 (Residues: 2-90; Coverage: 98%)
Gene names: SAOUHSC_02510, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: S
Molecule details ›
Chain: S
Length: 103 amino acids
Theoretical weight: 11.32 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW17 (Residues: 2-104; Coverage: 98%)
Gene names: SAOUHSC_02501, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: T
Molecule details ›
Chain: T
Length: 94 amino acids
Theoretical weight: 10.46 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FJE0 (Residues: 2-95; Coverage: 43%)
Gene names: SAUSA300_0479, ctc, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: U
Molecule details ›
Chain: U
Length: 79 amino acids
Theoretical weight: 8.6 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXT0 (Residues: 15-93; Coverage: 84%)
Gene names: SAOUHSC_01755, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: V
Molecule details ›
Chain: V
Length: 49 amino acids
Theoretical weight: 5.5 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZ60 (Residues: 12-60; Coverage: 79%)
Gene names: SAOUHSC_01191, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: W
Molecule details ›
Chain: W
Length: 67 amino acids
Theoretical weight: 7.85 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW14 (Residues: 2-68; Coverage: 97%)
Gene names: SAOUHSC_02504, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: X
Molecule details ›
Chain: X
Length: 58 amino acids
Theoretical weight: 6.43 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P0A0G2 (Residues: 2-59; Coverage: 98%)
Gene names: SAOUHSC_02493, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Structure domains: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein bL32 Chain: Z
Molecule details ›
Chain: Z
Length: 48 amino acids
Theoretical weight: 5.57 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZF1 (Residues: 2-50; Coverage: 83%)
Gene names: SAOUHSC_01078, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33A Chain: 1
Molecule details ›
Chain: 1
Length: 47 amino acids
Theoretical weight: 5.68 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FYU6 (Residues: 2-48; Coverage: 96%)
Gene names: SAOUHSC_01328, rpmG1
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 43 amino acids
Theoretical weight: 5.25 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FUQ0 (Residues: 2-44; Coverage: 96%)
Gene names: SAOUHSC_03055, rpmH
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 64 amino acids
Theoretical weight: 7.46 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXQ0 (Residues: 2-65; Coverage: 97%)
Gene names: SAOUHSC_01785, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 4
Molecule details ›
Chain: 4
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW29 (Residues: 1-37; Coverage: 100%)
Gene names: SAOUHSC_02488, rpmJ
Sequence domains: Ribosomal protein L36
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2923 nucleotides
Theoretical weight: 946.74 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 115 nucleotides
Theoretical weight: 36.97 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand MG 237 x MG
2 modified residues:
Ligand 5MU 2 x 5MU
Ligand 2MA 1 x 2MA

Experiments and Validation Details

Entry percentile scores
Resolution: 2.65Å
Relevant EMDB volumes: EMD-0243

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