6u48

Electron Microscopy
2.87Å resolution

E. coli 50S with phazolicin (PHZ) bound in exit tunnel

Released:
Entry authors: Watson ZL, Cate JHD, Polikanov YS, Severinov K
Related structures: EMD-20638

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
Entry contents:
30 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (32 distinct):
50S ribosomal protein L2 Chain: CC
Molecule details ›
Chain: CC
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A1X3I1Y9 (Residues: 2-272; Coverage: 99%)
Gene names: EAMG_04102, rplB
Sequence domains:
50S ribosomal protein L3 Chain: CD
Molecule details ›
Chain: CD
Length: 209 amino acids
Theoretical weight: 22.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A1X3JBR5 (Residues: 1-209; Coverage: 100%)
Gene names: ECVG_03084, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chain: CE
Molecule details ›
Chain: CE
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7Z9F6 (Residues: 1-201; Coverage: 100%)
Gene names: HMPREF9534_00849, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chain: CF
Molecule details ›
Chain: CF
Length: 177 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: V8K465 (Residues: 2-178; Coverage: 99%)
Gene names: V415_19085, rplE
Sequence domains:
50S ribosomal protein L6 Chain: CG
Molecule details ›
Chain: CG
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A080FKA9 (Residues: 2-177; Coverage: 99%)
Gene names: AD40_4004, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chain: CH
Molecule details ›
Chain: CH
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7ZI15 (Residues: 1-149; Coverage: 100%)
Gene names: HMPREF9534_03905, rplI
Sequence domains:
50S ribosomal protein L11 Chain: CJ
Molecule details ›
Chain: CJ
Length: 134 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: H4KQ36 (Residues: 8-141; Coverage: 94%)
Gene names: ECDEC2C_4834, rplK
Sequence domains: Ribosomal protein L11, RNA binding domain
50S ribosomal protein L13 Chain: CK
Molecule details ›
Chain: CK
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7ZET0 (Residues: 1-142; Coverage: 100%)
Gene names: HMPREF9534_02760, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: CL
Molecule details ›
Chain: CL
Length: 122 amino acids
Theoretical weight: 13.45 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A140N3H4 (Residues: 1-122; Coverage: 99%)
Gene names: ECBD_0441, rplN
50S ribosomal protein L16 Chain: CN
Molecule details ›
Chain: CN
Length: 136 amino acids
Theoretical weight: 15.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: J7RVN4 (Residues: 1-136; Coverage: 100%)
Gene names: BN16_39441, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chain: CO
Molecule details ›
Chain: CO
Length: 120 amino acids
Theoretical weight: 13.72 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A0A8UJP9 (Residues: 1-120; Coverage: 95%)
Gene names: ECO26H__620014, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chain: CP
Molecule details ›
Chain: CP
Length: 116 amino acids
Theoretical weight: 12.66 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: I2X628 (Residues: 2-117; Coverage: 99%)
Gene names: EC23916_1165, rplR
50S ribosomal protein L19 Chain: CQ
Molecule details ›
Chain: CQ
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: L2UTN8 (Residues: 2-115; Coverage: 99%)
Gene names: WCM_04782, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chain: CR
Molecule details ›
Chain: CR
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: I2RGN4 (Residues: 2-118; Coverage: 99%)
Gene names: EC12741_2131, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chain: CS
Molecule details ›
Chain: CS
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7ZEN7 (Residues: 1-103; Coverage: 100%)
Gene names: HMPREF9534_02716, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chain: CT
Molecule details ›
Chain: CT
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7Z9G0 (Residues: 1-110; Coverage: 100%)
Gene names: HMPREF9534_00853, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chain: CU
Molecule details ›
Chain: CU
Length: 93 amino acids
Theoretical weight: 10.55 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: H4IXX7 (Residues: 1-93; Coverage: 93%)
Gene names: ECDEC1C_4040, rplW
50S ribosomal protein L24 Chain: CV
Molecule details ›
Chain: CV
Length: 102 amino acids
Theoretical weight: 11.08 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A0G3K7Z5 (Residues: 2-103; Coverage: 98%)
Gene names: PPECC33_03627, rplX
Sequence domains:
50S ribosomal protein L25 Chain: CW
Molecule details ›
Chain: CW
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D7XH79 (Residues: 1-94; Coverage: 100%)
Gene names: HMPREF9536_00351, rplY
Sequence domains: Ribosomal L25p family
50S ribosomal protein L27 Chain: CX
Molecule details ›
Chain: CX
Length: 75 amino acids
Theoretical weight: 8.17 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A1X3JCC7 (Residues: 11-85; Coverage: 88%)
Gene names: ECVG_02038, rpmA
50S ribosomal protein L28 Chain: CY
Molecule details ›
Chain: CY
Length: 77 amino acids
Theoretical weight: 8.9 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: V8F9Y0 (Residues: 2-78; Coverage: 99%)
Gene names: Q458_28455, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chain: CZ
Molecule details ›
Chain: CZ
Length: 62 amino acids
Theoretical weight: 7.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: D8E8E5 (Residues: 2-63; Coverage: 98%)
Gene names: HMPREF9346_02732, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: C0
Molecule details ›
Chain: C0
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A073UEE9 (Residues: 2-59; Coverage: 98%)
Gene names: AB08_4684, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L32 Chain: C1
Molecule details ›
Chain: C1
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: V0ZMP5 (Residues: 2-57; Coverage: 98%)
Gene names: HMPREF1611_02371, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chain: C2
Molecule details ›
Chain: C2
Length: 50 amino acids
Theoretical weight: 5.81 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: L4V2B0 (Residues: 4-53; Coverage: 91%)
Gene names: WIC_04115, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chain: C3
Molecule details ›
Chain: C3
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: B7MGC4 (Residues: 1-46; Coverage: 100%)
Gene names: ECS88_4126, rpmH
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chain: C4
Molecule details ›
Chain: C4
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: I2RJ64 (Residues: 2-65; Coverage: 99%)
Gene names: EC12741_2130, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: C5
Molecule details ›
Chain: C5
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: A0A0E2L017 (Residues: 1-38; Coverage: 100%)
Gene names: G925_03522, rpmJ
Sequence domains: Ribosomal protein L36
phazolicin Chain: A
Molecule details ›
Chain: A
Length: 22 amino acids
Theoretical weight: 2.05 KDa
Source organism: Rhizobium sp. Pop5
23S ribosomal RNA Chain: CA
Molecule details ›
Chain: CA
Length: 2904 nucleotides
Theoretical weight: 941.09 KDa
5S ribosomal RNA Chain: CB
Molecule details ›
Chain: CB
Length: 118 nucleotides
Theoretical weight: 38.18 KDa

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
Resolution: 2.87Å
Relevant EMDB volumes: EMD-20638