› 6tc3

Electron Microscopy
2.7Å resolution

Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)

Released:
DOI: 10.2210/pdb6tc3/pdb
PDB entry 6tc3 coloured by chain, front view.
PDB entry 6tc3 coloured by chain, side view.
PDB entry 6tc3 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Ornithine capture by a translating ribosome controls bacterial polyamine synthesis.
Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA
Nat Microbiol 5 554-561 (2020)
PMID: 32094585
Related structures: EMD-10458

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-135684 (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Small ribosomal subunit protein uS2 Chain: S021
Molecule details ›
Chain: S021
Length: 241 amino acids
Theoretical weight: 26.78 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 1-241; Coverage: 100%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: S031
Molecule details ›
Chain: S031
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V3 (Residues: 1-233; Coverage: 100%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: S041
Molecule details ›
Chain: S041
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V8 (Residues: 1-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: S051
Molecule details ›
Chain: S051
Length: 167 amino acids
Theoretical weight: 17.63 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 1-167; Coverage: 100%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6 Chain: S061
Molecule details ›
Chain: S061
Length: 135 amino acids
Theoretical weight: 15.73 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-135; Coverage: 100%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: S071
Molecule details ›
Chain: S071
Length: 179 amino acids
Theoretical weight: 20.06 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02359 (Residues: 1-179; Coverage: 100%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: S081
Molecule details ›
Chain: S081
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W7 (Residues: 1-130; Coverage: 100%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: S091
Molecule details ›
Chain: S091
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7X3 (Residues: 1-130; Coverage: 100%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: S101
Molecule details ›
Chain: S101
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 1-103; Coverage: 100%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: S111
Molecule details ›
Chain: S111
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: S121
Molecule details ›
Chain: S121
Length: 124 amino acids
Theoretical weight: 13.81 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S3 (Residues: 1-124; Coverage: 100%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: S131
Molecule details ›
Chain: S131
Length: 118 amino acids
Theoretical weight: 13.13 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S9 (Residues: 1-118; Coverage: 100%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: S141
Molecule details ›
Chain: S141
Length: 102 amino acids
Theoretical weight: 11.68 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 1-35, 36-101; Coverage: 100%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: S151
Molecule details ›
Chain: S151
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ4 (Residues: 1-89; Coverage: 100%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: S161
Molecule details ›
Chain: S161
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: S171
Molecule details ›
Chain: S171
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG63 (Residues: 1-84; Coverage: 100%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: S181
Molecule details ›
Chain: S181
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 1-75; Coverage: 100%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S191
Molecule details ›
Chain: S191
Length: 92 amino acids
Theoretical weight: 10.46 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U3 (Residues: 1-92; Coverage: 100%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: S201
Molecule details ›
Chain: S201
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: S211
Molecule details ›
Chain: S211
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68679 (Residues: 1-71; Coverage: 100%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein uL2 Chain: L021
Molecule details ›
Chain: L021
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: L031
Molecule details ›
Chain: L031
Length: 209 amino acids
Theoretical weight: 22.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: L041
Molecule details ›
Chain: L041
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: L051
Molecule details ›
Chain: L051
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: L061
Molecule details ›
Chain: L061
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG55 (Residues: 1-177; Coverage: 100%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: L091
Molecule details ›
Chain: L091
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein bL31 Chain: L311
Molecule details ›
Chain: L311
Length: 70 amino acids
Theoretical weight: 7.89 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M9 (Residues: 1-70; Coverage: 100%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein uL13 Chain: L131
Molecule details ›
Chain: L131
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: L141
Molecule details ›
Chain: L141
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: L151
Molecule details ›
Chain: L151
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: L161
Molecule details ›
Chain: L161
Length: 136 amino acids
Theoretical weight: 15.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: L171
Molecule details ›
Chain: L171
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: L181
Molecule details ›
Chain: L181
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: L191
Molecule details ›
Chain: L191
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: L201
Molecule details ›
Chain: L201
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: L211
Molecule details ›
Chain: L211
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: L221
Molecule details ›
Chain: L221
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: L231
Molecule details ›
Chain: L231
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: L241
Molecule details ›
Chain: L241
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: L251
Molecule details ›
Chain: L251
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: L271
Molecule details ›
Chain: L271
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: L281
Molecule details ›
Chain: L281
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M2 (Residues: 1-78; Coverage: 100%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: L291
Molecule details ›
Chain: L291
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: L301
Molecule details ›
Chain: L301
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: L321
Molecule details ›
Chain: L321
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: L331
Molecule details ›
Chain: L331
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: L341
Molecule details ›
Chain: L341
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: L351
Molecule details ›
Chain: L351
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: L361
Molecule details ›
Chain: L361
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Leader peptide SpeFL Chain: SPE1
Molecule details ›
Chain: SPE1
Length: 34 amino acids
Theoretical weight: 4.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0DTV7 (Residues: 1-34; Coverage: 100%)
Gene names: b4803, speFL
16S ribosomal RNA Chain: 16S1
Molecule details ›
Chain: 16S1
Length: 1534 nucleotides
Theoretical weight: 497.4 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: 23S1
Molecule details ›
Chain: 23S1
Length: 2897 nucleotides
Theoretical weight: 939.61 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 05S1
Molecule details ›
Chain: 05S1
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
Messenger RNA Chain: MRN1
Molecule details ›
Chain: MRN1
Length: 7 nucleotides
Theoretical weight: 2.17 KDa
P-site Arg-tRNA Chain: PTR1
Molecule details ›
Chain: PTR1
Length: 76 nucleotides
Theoretical weight: 24.58 KDa
Sequence domains: tRNA

Ligands and Environments

5 bound ligands:
Ligand MG 339 x MG
Ligand K 147 x K
Ligand UNX 1201 x UNX
Ligand ZN 3 x ZN
Ligand ORN 1 x ORN
20 modified residues:
Ligand PSU 11 x PSU
Ligand G7M 3 x G7M
Ligand 2MG 6 x 2MG
Ligand 5MC 3 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand D2T 1 x D2T
Ligand 1MG 1 x 1MG
Ligand 5MU 3 x 5MU
Ligand 6MZ 2 x 6MZ
Ligand 3TD 1 x 3TD
Ligand OMG 1 x OMG
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4D4 1 x 4D4
Ligand FME 1 x FME
Ligand 4SU 1 x 4SU
Ligand RSP 1 x RSP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-10458

Quick links

Citations

7 review citations

Escherichia coli Small Proteome.
Hemm et al. (2020)
6 more

5 mentions without citation

Ornithine capture by a translating ribosome controls bacterial polyamine synthesis.
Herrero Del Valle et al. (2020)
4 more