Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 43-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopq 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 2105.55 kDa 
• Atom Count: 140969 
• Residue Count: 10837 
• Unique protein chains: 43
• Unique nucleic acid chains: 3

6Y6X

Tetracenomycin X bound to the human ribosome

• DOI: 10.2210/pdb6Y6X/pdb
• EMDataResource: EMD-10709

• Classification: ANTIBIOTIC
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2020-02-27 Released: 2020-07-08 
• Deposition Author(s): Buschauer, R., Cheng, J., Berninghausen, O., Beckmann, R., Wilson, D.N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.

Osterman, I.A., Wieland, M., Maviza, T.P., Lashkevich, K.A., Lukianov, D.A., Komarova, E.S., Zakalyukina, Y.V., Buschauer, R., Shiriaev, D.I., Leyn, S.A., Zlamal, J.E., Biryukov, M.V., Skvortsov, D.A., Tashlitsky, V.N., Polshakov, V.I., Cheng, J., Polikanov, Y.S., Bogdanov, A.A., Osterman, A.L., Dmitriev, S.E., Beckmann, R., Dontsova, O.A., Wilson, D.N., Sergiev, P.V.

(2020) Nat Chem Biol 

• PubMed: 32601485 
• DOI: 10.1038/s41589-020-0578-x
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The increase in multi-drug resistant pathogenic bacteria is making our current arsenal of clinically used antibiotics obsolete, highlighting the urgent need for new lead compounds with distinct target binding sites to avoid cross-resistance. Here we report that the aromatic polyketide antibiotic tetracenomycin (TcmX) is a potent inhibitor of protein synthesis, and does not induce DNA damage as previously thought. Despite the structural similarity to the well-known translation inhibitor tetracycline, we show that TcmX does not interact with the small ribosomal subunit, but rather binds to the large subunit, within the polypeptide exit tunnel. This previously unappreciated binding site is located adjacent to the macrolide-binding site, where TcmX stacks on the noncanonical basepair formed by U1782 and U2586 of the 23S ribosomal RNA. Although the binding site is distinct from the macrolide antibiotics, our results indicate that like macrolides, TcmX allows translation of short oligopeptides before further translation is blocked.

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Organizational Affiliation: 

Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. [e-mail].

Macromolecules

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L3	LB	397	Homo sapiens	Mutation(s): 0  Gene Names: RPL3, OK/SW-cl.32
Find proteins for P39023 (Homo sapiens) Explore P39023  Go to UniProtKB:  P39023
NIH Common Fund Data Resources
PHAROS  P39023 GTEx  ENSG00000100316

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L4	LC	368	Homo sapiens	Mutation(s): 0  Gene Names: RPL4, RPL1
Find proteins for P36578 (Homo sapiens) Explore P36578  Go to UniProtKB:  P36578
NIH Common Fund Data Resources
PHAROS  P36578 GTEx  ENSG00000174444

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L5	LD	293	Homo sapiens	Mutation(s): 0  Gene Names: RPL5, MSTP030
Find proteins for P46777 (Homo sapiens) Explore P46777  Go to UniProtKB:  P46777
NIH Common Fund Data Resources
PHAROS  P46777 GTEx  ENSG00000122406

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L6	LE	247	Homo sapiens	Mutation(s): 0  Gene Names: RPL6, TXREB1
Find proteins for Q02878 (Homo sapiens) Explore Q02878  Go to UniProtKB:  Q02878
NIH Common Fund Data Resources
PHAROS  Q02878 GTEx  ENSG00000089009

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7	LF	225	Homo sapiens	Mutation(s): 0  Gene Names: RPL7
Find proteins for P18124 (Homo sapiens) Explore P18124  Go to UniProtKB:  P18124
NIH Common Fund Data Resources
PHAROS  P18124 GTEx  ENSG00000147604

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L9	LH	190	Homo sapiens	Mutation(s): 0  Gene Names: RPL9, OK/SW-cl.103, RPL9P7, RPL9P8, RPL9P9
Find proteins for P32969 (Homo sapiens) Explore P32969  Go to UniProtKB:  P32969
NIH Common Fund Data Resources
PHAROS  P32969 GTEx  ENSG00000163682

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L10-like	LI	213	Homo sapiens	Mutation(s): 0  Gene Names: RPL10L
Find proteins for Q96L21 (Homo sapiens) Explore Q96L21  Go to UniProtKB:  Q96L21
NIH Common Fund Data Resources
PHAROS  Q96L21 GTEx  ENSG00000165496

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L11	LJ	176	Homo sapiens	Mutation(s): 0  Gene Names: RPL11
Find proteins for P62913 (Homo sapiens) Explore P62913  Go to UniProtKB:  P62913
NIH Common Fund Data Resources
PHAROS  P62913 GTEx  ENSG00000142676

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13	LL	210	Homo sapiens	Mutation(s): 0  Gene Names: RPL13, BBC1, OK/SW-cl.46
Find proteins for P26373 (Homo sapiens) Explore P26373  Go to UniProtKB:  P26373
NIH Common Fund Data Resources
PHAROS  P26373 GTEx  ENSG00000167526

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13a	LO	201	Homo sapiens	Mutation(s): 0  Gene Names: RPL13A
Find proteins for P40429 (Homo sapiens) Explore P40429  Go to UniProtKB:  P40429
NIH Common Fund Data Resources
PHAROS  P40429 GTEx  ENSG00000142541

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L17	LP	153	Homo sapiens	Mutation(s): 0  Gene Names: RPL17
Find proteins for P18621 (Homo sapiens) Explore P18621  Go to UniProtKB:  P18621
NIH Common Fund Data Resources
PHAROS  P18621 GTEx  ENSG00000265681

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L18	LQ	187	Homo sapiens	Mutation(s): 0  Gene Names: RPL18
Find proteins for Q07020 (Homo sapiens) Explore Q07020  Go to UniProtKB:  Q07020
NIH Common Fund Data Resources
PHAROS  Q07020 GTEx  ENSG00000063177

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L19	LR	187	Homo sapiens	Mutation(s): 0  Gene Names: RPL19
Find proteins for P84098 (Homo sapiens) Explore P84098  Go to UniProtKB:  P84098
NIH Common Fund Data Resources
PHAROS  P84098 GTEx  ENSG00000108298

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L18a	LS	175	Homo sapiens	Mutation(s): 0  Gene Names: RPL18A
Find proteins for Q02543 (Homo sapiens) Explore Q02543  Go to UniProtKB:  Q02543
NIH Common Fund Data Resources
GTEx  ENSG00000105640

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L21	LT	159	Homo sapiens	Mutation(s): 0  Gene Names: RPL21
Find proteins for P46778 (Homo sapiens) Explore P46778  Go to UniProtKB:  P46778
NIH Common Fund Data Resources
PHAROS  P46778 GTEx  ENSG00000122026

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L22	LU	99	Homo sapiens	Mutation(s): 0  Gene Names: RPL22
Find proteins for P35268 (Homo sapiens) Explore P35268  Go to UniProtKB:  P35268
NIH Common Fund Data Resources
PHAROS  P35268 GTEx  ENSG00000116251

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L23	LV	131	Homo sapiens	Mutation(s): 0  Gene Names: RPL23
Find proteins for P62829 (Homo sapiens) Explore P62829  Go to UniProtKB:  P62829
NIH Common Fund Data Resources
PHAROS  P62829 GTEx  ENSG00000125691

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L24	LW	124	Homo sapiens	Mutation(s): 0  Gene Names: RPL24
Find proteins for P83731 (Homo sapiens) Explore P83731  Go to UniProtKB:  P83731
NIH Common Fund Data Resources
PHAROS  P83731 GTEx  ENSG00000114391

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L23a	LX	120	Homo sapiens	Mutation(s): 0  Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens) Explore P62750  Go to UniProtKB:  P62750
NIH Common Fund Data Resources
PHAROS  P62750 GTEx  ENSG00000198242

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L26	LY	134	Homo sapiens	Mutation(s): 0  Gene Names: RPL26
Find proteins for P61254 (Homo sapiens) Explore P61254  Go to UniProtKB:  P61254
NIH Common Fund Data Resources
PHAROS  P61254 GTEx  ENSG00000161970

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L27	LZ	135	Homo sapiens	Mutation(s): 0  Gene Names: RPL27
Find proteins for P61353 (Homo sapiens) Explore P61353  Go to UniProtKB:  P61353
NIH Common Fund Data Resources
PHAROS  P61353 GTEx  ENSG00000131469

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L27a	La	147	Homo sapiens	Mutation(s): 0  Gene Names: RPL27A
Find proteins for P46776 (Homo sapiens) Explore P46776  Go to UniProtKB:  P46776
NIH Common Fund Data Resources
PHAROS  P46776 GTEx  ENSG00000166441

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L29	Lb	121	Homo sapiens	Mutation(s): 0  Gene Names: RPL29
Find proteins for P47914 (Homo sapiens) Explore P47914  Go to UniProtKB:  P47914
NIH Common Fund Data Resources
GTEx  ENSG00000162244

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L30	Lc	98	Homo sapiens	Mutation(s): 0  Gene Names: RPL30
Find proteins for P62888 (Homo sapiens) Explore P62888  Go to UniProtKB:  P62888
NIH Common Fund Data Resources
PHAROS  P62888 GTEx  ENSG00000156482

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L31	Ld	107	Homo sapiens	Mutation(s): 0  Gene Names: RPL31
Find proteins for P62899 (Homo sapiens) Explore P62899  Go to UniProtKB:  P62899
NIH Common Fund Data Resources
PHAROS  P62899 GTEx  ENSG00000071082

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L32	Le	128	Homo sapiens	Mutation(s): 0  Gene Names: RPL32, PP9932
Find proteins for P62910 (Homo sapiens) Explore P62910  Go to UniProtKB:  P62910
NIH Common Fund Data Resources
PHAROS  P62910 GTEx  ENSG00000144713

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L35a	Lf	109	Homo sapiens	Mutation(s): 0  Gene Names: RPL35A, GIG33
Find proteins for P18077 (Homo sapiens) Explore P18077  Go to UniProtKB:  P18077
NIH Common Fund Data Resources
PHAROS  P18077 GTEx  ENSG00000182899

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L35	Lh	122	Homo sapiens	Mutation(s): 0  Gene Names: RPL35
Find proteins for P42766 (Homo sapiens) Explore P42766  Go to UniProtKB:  P42766
NIH Common Fund Data Resources
PHAROS  P42766 GTEx  ENSG00000136942

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L37	Lj	86	Homo sapiens	Mutation(s): 0  Gene Names: RPL37
Find proteins for P61927 (Homo sapiens) Explore P61927  Go to UniProtKB:  P61927
NIH Common Fund Data Resources
PHAROS  P61927 GTEx  ENSG00000145592

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L38	Lk	69	Homo sapiens	Mutation(s): 0  Gene Names: RPL38
Find proteins for P63173 (Homo sapiens) Explore P63173  Go to UniProtKB:  P63173
NIH Common Fund Data Resources
PHAROS  P63173 GTEx  ENSG00000172809

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L39	Ll	50	Homo sapiens	Mutation(s): 0  Gene Names: RPL39
Find proteins for P62891 (Homo sapiens) Explore P62891  Go to UniProtKB:  P62891
NIH Common Fund Data Resources
PHAROS  P62891 GTEx  ENSG00000198918

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-60S ribosomal protein L40	Lm	52	Homo sapiens	Mutation(s): 0  Gene Names: UBA52, UBCEP2
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987 GTEx  ENSG00000221983

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L41	Ln	24	Homo sapiens	Mutation(s): 0  Gene Names: RPL41
Find proteins for P62945 (Homo sapiens) Explore P62945  Go to UniProtKB:  P62945
NIH Common Fund Data Resources
PHAROS  P62945 GTEx  ENSG00000229117

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L36a	Lo	105	Homo sapiens	Mutation(s): 0  Gene Names: RPL36A, RPL44, GIG15, MIG6
Find proteins for P83881 (Homo sapiens) Explore P83881  Go to UniProtKB:  P83881
NIH Common Fund Data Resources
PHAROS  P83881

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L28	Lr	125	Homo sapiens	Mutation(s): 0  Gene Names: RPL28
Find proteins for P46779 (Homo sapiens) Explore P46779  Go to UniProtKB:  P46779
NIH Common Fund Data Resources
PHAROS  P46779 GTEx  ENSG00000108107

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L10a	Lz	217	Homo sapiens	Mutation(s): 0  Gene Names: RPL10A, NEDD6
Find proteins for P62906 (Homo sapiens) Explore P62906  Go to UniProtKB:  P62906
NIH Common Fund Data Resources
PHAROS  P62906 GTEx  ENSG00000198755

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7a	LG	241	Homo sapiens	Mutation(s): 0  Gene Names: RPL7A, SURF-3, SURF3
Find proteins for P62424 (Homo sapiens) Explore P62424  Go to UniProtKB:  P62424
NIH Common Fund Data Resources
PHAROS  P62424 GTEx  ENSG00000148303

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L14	LM	139	Homo sapiens	Mutation(s): 0  Gene Names: RPL14
Find proteins for P50914 (Homo sapiens) Explore P50914  Go to UniProtKB:  P50914
NIH Common Fund Data Resources
PHAROS  P50914 GTEx  ENSG00000188846

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L15	LN	203	Homo sapiens	Mutation(s): 0  Gene Names: RPL15, EC45, TCBAP0781
Find proteins for P61313 (Homo sapiens) Explore P61313  Go to UniProtKB:  P61313
NIH Common Fund Data Resources
PHAROS  P61313 GTEx  ENSG00000174748

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L34	Lg	114	Homo sapiens	Mutation(s): 0  Gene Names: RPL34
Find proteins for P49207 (Homo sapiens) Explore P49207  Go to UniProtKB:  P49207
NIH Common Fund Data Resources
PHAROS  P49207 GTEx  ENSG00000109475

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L36	Li	102	Homo sapiens	Mutation(s): 0  Gene Names: RPL36
Find proteins for Q9Y3U8 (Homo sapiens) Explore Q9Y3U8  Go to UniProtKB:  Q9Y3U8
NIH Common Fund Data Resources
PHAROS  Q9Y3U8 GTEx  ENSG00000130255

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8	LA	248	Homo sapiens	Mutation(s): 0  Gene Names: RPL8
Find proteins for P62917 (Homo sapiens) Explore P62917  Go to UniProtKB:  P62917
NIH Common Fund Data Resources
PHAROS  P62917 GTEx  ENSG00000161016

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L37a	Lp	91	Homo sapiens	Mutation(s): 0  Gene Names: RPL37A
Find proteins for P61513 (Homo sapiens) Explore P61513  Go to UniProtKB:  P61513
NIH Common Fund Data Resources
PHAROS  P61513 GTEx  ENSG00000197756

Entity ID: 1
Molecule	Chains	Length	Organism
28S ribosomal RNA	L5	3773	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism
5S ribosomal RNA	L7	120	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism
5.8S ribosomal RNA	L8	156	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OCW	L5	methyl (6~{a}~{R},7~{S},10~{a}~{R})-3,8,10~{a}-trimethoxy-1-methyl-6~{a},7,12-tris(oxidanyl)-6,10,11-tris(oxidanylidene)-7~{H}-tetracene-2-carboxylate C24 H22 O11 QSPIPUXWSNFXCK-AGILITTLSA-N
ZN	Lg, Lj, Lm, Lo, Lp	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	L5, L7, L8, LA, LI, LP, LT, LV, Le, Lg, Lj	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-02-27 
• Released Date: 2020-07-08 
Deposition Author(s): Buschauer, R., Cheng, J., Berninghausen, O., Beckmann, R., Wilson, D.N.

Revision History 

• Version 1.0: 2020-07-08
  Type: Initial release