› 7m4w

Electron Microscopy
2.55Å resolution

A. baumannii Ribosome-Eravacycline complex: Empty 70S

Released:
DOI: 10.2210/pdb7m4w/pdb
PDB entry 7m4w coloured by chain, front view.
PDB entry 7m4w coloured by chain, side view.
PDB entry 7m4w coloured by chain, top view.
Source organism: Acinetobacter baumannii AB0057
Primary publication:
Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
Zhang Z, Morgan CE, Bonomo RA, Yu EW
mBio 12 e0103121 (2021)
PMID: 34044590
Related structures: EMD-23668

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 51-mer (preferred)
PDBe Complex ID:
PDB-CPX-236569 (preferred)
Entry contents:
48 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (51 distinct):
50S ribosomal protein L33 Chain: 0
Molecule details ›
Chain: 0
Length: 51 amino acids
Theoretical weight: 6.11 KDa
Source organism: Acinetobacter baumannii AB0057
Large ribosomal subunit protein bL34 Chain: 1
Molecule details ›
Chain: 1
Length: 44 amino acids
Theoretical weight: 5.19 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: A0A014CLK2 (Residues: 1-44; Coverage: 100%)
Gene names: J804_3540, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 2
Molecule details ›
Chain: 2
Length: 64 amino acids
Theoretical weight: 7.42 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I693 (Residues: 1-64; Coverage: 100%)
Gene names: AB57_0700, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: 3
Molecule details ›
Chain: 3
Length: 38 amino acids
Theoretical weight: 4.28 KDa
Source organism: Acinetobacter baumannii AB0057
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 274 amino acids
Theoretical weight: 30.35 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA36 (Residues: 1-274; Coverage: 100%)
Gene names: AB57_3527, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 212 amino acids
Theoretical weight: 22.51 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA39 (Residues: 1-212; Coverage: 100%)
Gene names: AB57_3530, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 200 amino acids
Theoretical weight: 21.58 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA38 (Residues: 1-200; Coverage: 100%)
Gene names: AB57_3529, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 178 amino acids
Theoretical weight: 20.05 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA27 (Residues: 1-178; Coverage: 100%)
Gene names: AB57_3518, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 19.13 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA24 (Residues: 1-177; Coverage: 100%)
Gene names: AB57_3515, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 148 amino acids
Theoretical weight: 15.8 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IBC3 (Residues: 1-148; Coverage: 100%)
Gene names: AB57_2511, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chain: I
Molecule details ›
Chain: I
Length: 142 amino acids
Theoretical weight: 15.98 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I9B0 (Residues: 1-142; Coverage: 100%)
Gene names: AB57_3451, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: J
Molecule details ›
Chain: J
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: N9NZ44 (Residues: 1-122; Coverage: 100%)
Gene names: F897_01028, F969_03557, IAQ69_12965, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: K
Molecule details ›
Chain: K
Length: 146 amino acids
Theoretical weight: 15.51 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA20 (Residues: 1-146; Coverage: 100%)
Gene names: AB57_3511, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: L
Molecule details ›
Chain: L
Length: 137 amino acids
Theoretical weight: 15.5 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA32 (Residues: 1-137; Coverage: 100%)
Gene names: AB57_3523, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: M
Molecule details ›
Chain: M
Length: 125 amino acids
Theoretical weight: 14.02 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA13 (Residues: 1-125; Coverage: 100%)
Gene names: AB57_3504, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: N
Molecule details ›
Chain: N
Length: 116 amino acids
Theoretical weight: 12.44 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA23 (Residues: 1-116; Coverage: 100%)
Gene names: AB57_3514, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: O
Molecule details ›
Chain: O
Length: 122 amino acids
Theoretical weight: 13.62 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IAS9 (Residues: 1-122; Coverage: 100%)
Gene names: AB57_3615, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: P
Molecule details ›
Chain: P
Length: 119 amino acids
Theoretical weight: 13.47 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: V5VGC9 (Residues: 1-119; Coverage: 100%)
Gene names: A7M90_00135, ABR2091_0624, ABUW_3284, APD17_02025, AUO97_10420, B9W25_05540, B9X95_03065, CAS83_19455, CBE85_16220, CV954_016800, DOL94_09815, EA686_12335, EA706_04480, EA722_13770, F2P40_14925, F4T85_10105, FJU42_08615, G3N53_02985, GNY86_20015, GSE42_03220, IAG11_09365, IMO23_03050, ITE13_07970, JHZ39_000459, MKP18_001477, P9867_10845, SAMEA104305318_00030, SAMEA4394745_03106, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: Q
Molecule details ›
Chain: Q
Length: 103 amino acids
Theoretical weight: 11.5 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I6V9 (Residues: 1-103; Coverage: 100%)
Gene names: AB57_3151, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: R
Molecule details ›
Chain: R
Length: 109 amino acids
Theoretical weight: 11.83 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: A0A009I821 (Residues: 1-109; Coverage: 100%)
Gene names: J512_1173, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: S
Molecule details ›
Chain: S
Length: 106 amino acids
Theoretical weight: 11.61 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA37 (Residues: 1-106; Coverage: 100%)
Gene names: AB57_3528, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: T
Molecule details ›
Chain: T
Length: 105 amino acids
Theoretical weight: 11.19 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA28 (Residues: 1-105; Coverage: 100%)
Gene names: AB57_3519, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: U
Molecule details ›
Chain: U
Length: 98 amino acids
Theoretical weight: 10.94 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I7B6 (Residues: 1-98; Coverage: 100%)
Gene names: AB57_0881, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: V
Molecule details ›
Chain: V
Length: 85 amino acids
Theoretical weight: 9.07 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I6V8 (Residues: 1-85; Coverage: 100%)
Gene names: AB57_3150, rpmA
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L28 Chain: W
Molecule details ›
Chain: W
Length: 78 amino acids
Theoretical weight: 9.13 KDa
Source organism: Acinetobacter baumannii AB0057
Large ribosomal subunit protein uL29 Chain: X
Molecule details ›
Chain: X
Length: 65 amino acids
Theoretical weight: 7.45 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA31 (Residues: 1-65; Coverage: 100%)
Gene names: AB57_3522, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: Y
Molecule details ›
Chain: Y
Length: 58 amino acids
Theoretical weight: 6.65 KDa
Source organism: Acinetobacter baumannii AB0057
Large ribosomal subunit protein bL32 Chain: Z
Molecule details ›
Chain: Z
Length: 61 amino acids
Theoretical weight: 7.1 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I7A4 (Residues: 1-61; Coverage: 100%)
Gene names: AB57_0869, rpmF
Sequence domains: Ribosomal L32p protein family
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 250 amino acids
Theoretical weight: 27.68 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: V5VBC2 (Residues: 1-250; Coverage: 100%)
Gene names: A7M90_04810, ABR2091_2511, ABUW_1235, APD17_10225, AUO97_00545, B9W25_05725, B9X95_11710, CAS83_20675, CBE85_00460, CV954_005970, DOL94_04645, EA706_00950, EA722_08625, F2P40_02015, F4T85_00580, FJU42_15265, G3N53_09920, GNY86_13625, GSE42_14090, IAG11_02475, IMO23_12420, ITE13_14320, JHZ39_000921, MKP18_000954, P9867_17040, SAMEA104305318_02019, SAMEA4394745_01929, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 250 amino acids
Theoretical weight: 27.97 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: V5V9N0 (Residues: 1-250; Coverage: 100%)
Gene names: A7M90_14915, ABR2091_3270, ABUW_0412, APD17_09550, AUO97_04375, B9W25_03435, B9X95_19970, CAS83_02350, CBE85_05920, CV954_002220, DOL94_03730, EA706_02770, EA722_02260, F2P40_01515, F4T85_12690, FJU42_03455, G3N53_17775, GNY86_00800, GSE42_17945, IAG11_07125, IMO23_15980, ITE13_06030, JHZ39_001290, MKP18_001993, SAMEA104305318_02210, SAMEA4394745_00245, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 208 amino acids
Theoretical weight: 23.31 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA15 (Residues: 1-208; Coverage: 100%)
Gene names: AB57_3506, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 165 amino acids
Theoretical weight: 17.18 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA22 (Residues: 1-165; Coverage: 100%)
Gene names: AB57_3513, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 127 amino acids
Theoretical weight: 14.99 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IBC1 (Residues: 1-127; Coverage: 100%)
Gene names: AB57_2509, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.73 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I7S0 (Residues: 1-156; Coverage: 100%)
Gene names: AB57_0912, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 131 amino acids
Theoretical weight: 14.25 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA25 (Residues: 1-131; Coverage: 100%)
Gene names: AB57_3516, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 128 amino acids
Theoretical weight: 14.29 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: V5VBA5 (Residues: 1-128; Coverage: 100%)
Gene names: A7M90_18075, ABR2091_3190, ABUW_0493, APD17_00075, AUO97_03980, B9W25_16350, B9X95_20200, CAS83_08535, CBE85_18930, CV954_019000, DOL94_17890, EA686_21355, EA706_14375, EA722_14435, F2P40_19085, F4T85_18570, FJU42_18715, G3N53_18265, GNY86_08815, GSE42_17575, IAG11_16000, IMO23_15560, ITE13_18750, JHZ39_003293, MKP18_003749, P9867_16165, SAMEA104305318_03848, SAMEA4394745_03633, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chain: j
Molecule details ›
Chain: j
Length: 103 amino acids
Theoretical weight: 11.72 KDa
Source organism: Acinetobacter baumannii AB0057
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 128 amino acids
Theoretical weight: 13.56 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: A0A4R0F9S8 (Residues: 1-128; Coverage: 100%)
Gene names: E0H89_13485, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I7R9 (Residues: 1-124; Coverage: 100%)
Gene names: AB57_0911, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.3 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA17 (Residues: 1-118; Coverage: 100%)
Gene names: AB57_3508, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 101 amino acids
Theoretical weight: 11.44 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA26 (Residues: 1-101; Coverage: 100%)
Gene names: AB57_3517, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.15 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I3U0 (Residues: 1-89; Coverage: 100%)
Gene names: AB57_0438, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 101 amino acids
Theoretical weight: 11.22 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: A0A1V3DIZ9 (Residues: 1-101; Coverage: 100%)
Gene names: AUO97_04820, B9W25_02995, B9X95_19530, CAS83_10135, CBE85_06365, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 85 amino acids
Theoretical weight: 9.54 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA30 (Residues: 1-85; Coverage: 100%)
Gene names: AB57_3521, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chain: r
Molecule details ›
Chain: r
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Acinetobacter baumannii AB0057
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 91 amino acids
Theoretical weight: 10.21 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7IA35 (Residues: 1-91; Coverage: 100%)
Gene names: AB57_3526, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 88 amino acids
Theoretical weight: 9.72 KDa
Source organism: Acinetobacter baumannii AB0057
UniProt:
  • Canonical: B7I5N9 (Residues: 1-88; Coverage: 100%)
Gene names: AB57_1842, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein S21 Chain: u
Molecule details ›
Chain: u
Length: 71 amino acids
Theoretical weight: 8.47 KDa
Source organism: Acinetobacter baumannii AB0057
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2918 nucleotides
Theoretical weight: 945.31 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 115 nucleotides
Theoretical weight: 37 KDa
Sequence domains: 5S ribosomal RNA
16s Ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1544 nucleotides
Theoretical weight: 500.3 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand YQM 3 x YQM
Ligand MG 191 x MG
13 modified residues:
Ligand PSU 8 x PSU
Ligand 3TD 1 x 3TD
Ligand 5MU 1 x 5MU
Ligand 6MZ 1 x 6MZ
Ligand G7M 2 x G7M
Ligand OMG 1 x OMG
Ligand 2MG 3 x 2MG
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 5MC 1 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.55Å
Relevant EMDB volumes: EMD-23668

Quick links

Citations

3 review citations

Drug‑resistant Acinetobacter baumannii: From molecular mechanisms to potential therapeutics (Review).
Wu et al. (2023)
2 more

2 mentions without citation

Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
Zhang et al. (2021)
1 more