Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxy Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer -A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwx 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 49-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvw Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 49-mer -A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuv 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4419077.50 
• Atom Count: 292307 
• Residue Count: 21699 
• Unique protein chains: 51
• Unique nucleic acid chains: 5

4WOI

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2

• DOI: 10.2210/pdb4WOI/pdb
• NDB: 4WOI

• Classification: RIBOSOME
• Organism(s): Escherichia coli (strain K12), Escherichia coli str. K-12 substr. MDS42, Enterobacteria phage L1, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)


• Deposited: 2014-10-15 Released: 2015-08-05 
• Deposition Author(s): Pulk, A., Cate, J.H.D., Blanchard, S., Wasserman, M., Altman, R., Zhou, Z., Zinder, J., Green, K., Garneau-Tsodikova, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Cancer Institute; Human Frontiers in Science Program; National Science Foundation (United States); Department of Energy (United States) 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.174 

Literature

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.

Wasserman, M.R., Pulk, A., Zhou, Z., Altman, R.B., Zinder, J.C., Green, K.D., Garneau-Tsodikova, S., Doudna Cate, J.H., Blanchard, S.C.

(2015) Nat Commun 6: 7896-7896

• PubMed: 26224058 
• DOI: 10.1038/ncomms8896


• PubMed Abstract: 
  

Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.

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Organizational Affiliation: 

Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	AB, DB	241	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S3	AC, DC	233	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S4	AD, DD	206	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S5	AE, DE	167	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7W1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	AF, DF	135	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12)) Go to UniProtKB:  P02358

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	AG, DG	179	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12)) Go to UniProtKB:  P02359

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S8	AH, DH	130	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7W7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S9	AI, DI	130	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7X3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S10	AJ, DJ	103	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R5

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	AK, DK	129	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R9

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S12	AL, DL	124	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7S3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S13	AM, DM	118	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7S9

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S14	AN, DN	101	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG59

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S15	AO, DO	89	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S16	AP, DP	82	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S17	AQ, DQ	84	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG63

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	AR, DR	75	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T7

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S19	AS, DS	92	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U3

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S20	AT, DT	87	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U7

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S21	AU, DU	71	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12)) Go to UniProtKB:  P68679

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
Ribosome-recycling factor	AV	185	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: frr (rrf)
Find proteins for P0A805 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A805

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	BC, CC	273	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12)) Go to UniProtKB:  P60422

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	BD, CD	209	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12)) Go to UniProtKB:  P60438

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	BE, CE	201	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12)) Go to UniProtKB:  P60723

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	BF, CF	179	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12)) Go to UniProtKB:  P62399

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	BG, CG	177	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG55

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	BH, CH	149	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R1

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L11	BI, CI	142	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7J7

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	BJ, CJ	142	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AA10

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	BK, CK	123	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY3

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	BL, CL	144	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12)) Go to UniProtKB:  P02413

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	BM, CM	136	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY7

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	BN, CN	127	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG44

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	BO, CO	117	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12)) Go to UniProtKB:  P0C018

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	BP, CP	115	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7K6

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	BQ, CQ	118	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L3

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21	BR, CR	103	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG48

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	BS, CS	110	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12)) Go to UniProtKB:  P61175

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	BT, CT	100	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADZ0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	BU, CU	104	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12)) Go to UniProtKB:  P60624

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	BV, CV	94	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12)) Go to UniProtKB:  P68919

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	BW, CW	85	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L8

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	BX, CX	78	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M2

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	BY, CY	63	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M6

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	BZ, CZ	59	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG51

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	B0, C0	57	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N4

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	B1, C1	55	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N9

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	B2, C2	46	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7P5

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	B3, C3	65	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q1

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L36	B4, C4	38	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q6

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L1	B5	228	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLP7

Entity ID: 1
Molecule	Chains	Length	Organism
16S ribosomal RNA	AA,DA	1542	Escherichia coli str. K-12 substr. MDS42

Entity ID: 23
Molecule	Chains	Length	Organism
Messenger RNA	AW,DV	16	Enterobacteria phage L1

Entity ID: 24
Molecule	Chains	Length	Organism
Phenylalanine specific transfer RNA, tRNA-Phe	AX,DW	76	Escherichia coli str. K-12 substr. MDS42

Entity ID: 25
Molecule	Chains	Length	Organism
23S ribosomal RNA	BA,CA	2904	Escherichia coli str. K-12 substr. MDS42

Entity ID: 26
Molecule	Chains	Length	Organism
5S ribosomal RNA	BB,CB	120	Escherichia coli str. K-12 substr. MDS42

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	B4, C4	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
PAR	AA, BA, CA, DA	PAROMOMYCIN PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
MG	AA, AN, BA, BB, BL, BO, BQ, CA, CB, CD, CQ, DA, DD, DN	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.253 
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 212.100	α = 90.00
b = 435.240	β = 90.00
c = 614.440	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-10-15 
• Released Date: 2015-08-05 
• Deposition Author(s): Pulk, A., Cate, J.H.D., Blanchard, S., Wasserman, M., Altman, R., Zhou, Z., Zinder, J., Green, K., Garneau-Tsodikova, S.

---

Funding Organization	Country	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	2R01GM079238
National Institutes of Health/National Institute of General Medical Sciences	United States	1R01GM65050
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	1R01AI090048
National Institutes of Health/National Cancer Institute	United States	CA92584
Human Frontiers in Science Program	United States	RGY0088
National Science Foundation (United States)	United States	0644129
Department of Energy (United States)	United States	DE-AC0376SF00098

Revision History 

• Version 1.0: 2015-08-05
  Type: Initial release
• Version 1.1: 2015-08-12
  Type: Database references
• Version 1.2: 2017-09-20
  Type: Author supporting evidence, Derived calculations, Refinement description