2ZJP: Thiopeptide antibiotic Nosiheptide

Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans. Determined by X-ray diffraction at 3.7 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 3.7 Å
Organisms: DEINOCOCCUS RADIODURANS, STREPTOMYCES ACTUOSUS
Chains: 31
Atoms: 84,444
Mol. weight: 1366.82 kDa
Ligands: ZN, MG, NO1
Released: 17 Jun 2008

Explore 2ZJP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZJP contains 84 α-helices and 182 β-strands across 25 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 4: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	3
β-strand	15	1	4
β-strand	24-25	2	3
β-strand	26	1	4
β-strand	34-35	2	3

Chain A: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	44	1	7
β-strand	49	1	7
β-strand	76-85	10	8
β-strand	90-97	8	8
β-strand	105-106	2	8
β-strand	116-118	3	8
β-strand	127	1	9
β-strand	130	1	9
β-strand	142-143	2	9
β-strand	163	1	9
β-strand	165-168	4	10
β-strand	172-176	5	10
β-strand	182-186	5	10
β-strand	192-193	2	9
α-helix	211-214	4
α-helix	223-225	3
α-helix	262-265	4
β-strand	267-268	2	10

Chain B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	11
β-strand	21-27	7	11
β-strand	31-32	2	12
β-strand	33-37	5	13
β-strand	46-50	5	13
α-helix	56-58	3
α-helix	61-68	8
β-strand	78-79	2	13
β-strand	89-90	2	12
β-strand	101-107	7	11
α-helix	108-109	2
β-strand	110-113	4	14
β-strand	159-161	3	14
β-strand	164-166	3	11
β-strand	170-171	2	11
β-strand	174-176	3	11
β-strand	181-185	5	11
β-strand	195-200	6	11

Chain C: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-38	15
α-helix	94-96	3
α-helix	97-112	16
β-strand	118	1	15
α-helix	131-138	8
β-strand	149-151	3	16
α-helix	155-158	4
β-strand	169-170	2	16
α-helix	177-182	6
β-strand	186-187	2	16
β-strand	189	1	15

Chain D: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
α-helix	8-12	5
α-helix	13-17	5
β-strand	33-37	5	17
α-helix	49-57	9
α-helix	58-62	5
α-helix	64-65	2
β-strand	66	1	18
β-strand	69	1	19
β-strand	84	1	19
β-strand	88	1	18
β-strand	90-91	2	17
α-helix	94-102	9
α-helix	103-107	5
β-strand	117	1	20
β-strand	129-130	2	17
α-helix	143-145	3
β-strand	153-157	5	17
α-helix	163-173	11
β-strand	177	1	20

Chain E: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	21
β-strand	23-26	4	21
β-strand	33-36	4	21
β-strand	44	1	22
β-strand	51	1	22
α-helix	60-81	22
β-strand	83-90	8	23
β-strand	95-96	2	24
β-strand	99	1	25
β-strand	102	1	25
β-strand	104-106	3	24
β-strand	113-114	2	24
β-strand	121-124	4	23
β-strand	130-135	6	23
α-helix	138-151	14
α-helix	153-155	3
β-strand	161-163	3	23

Chain F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	26
α-helix	35-44	10
β-strand	55-57	3	26
β-strand	59	1	27
β-strand	65	1	27
β-strand	68-69	2	26
α-helix	75-82	8
β-strand	97-98	2	28
α-helix	101-104	4
α-helix	121-134	14
β-strand	136-137	2	28
α-helix	138-139	2

Chain G: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	29
α-helix	51-63	13
β-strand	79-83	5	29
β-strand	99-102	4	30
β-strand	112-115	4	30
α-helix	116-118	3
α-helix	123-131	9
α-helix	139-145	7
β-strand	148-150	3	29
α-helix	157-160	4

17 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L33	1	protein	55	DEINOCOCCUS RADIODURANS	Q9RSS4 (AlphaFold model)
50S ribosomal protein L34	2	protein	47	DEINOCOCCUS RADIODURANS	Q9RSH2 (AlphaFold model)
50S ribosomal protein L35	3	protein	66	DEINOCOCCUS RADIODURANS	Q9RSW6 (AlphaFold model)
50S ribosomal protein L36	4	protein	37	DEINOCOCCUS RADIODURANS	Q9RSK0 (AlphaFold model)
Nosiheptide	5	protein	13	STREPTOMYCES ACTUOSUS	C6FX52
50S ribosomal protein L2	A	protein	274	DEINOCOCCUS RADIODURANS	Q9RXJ9
50S ribosomal protein L3	B	protein	211	DEINOCOCCUS RADIODURANS	Q9RXK2
50S ribosomal protein L4	C	protein	205	DEINOCOCCUS RADIODURANS	Q9RXK1
50S ribosomal protein L5	D	protein	180	DEINOCOCCUS RADIODURANS	Q9RXJ0
50S ribosomal protein L6	E	protein	185	DEINOCOCCUS RADIODURANS	Q9RSL3
50S ribosomal protein L11	F	protein	144	DEINOCOCCUS RADIODURANS	Q9RSS7
50S ribosomal protein L13	G	protein	174	DEINOCOCCUS RADIODURANS	Q9RXY1

19 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>2ZJP_1 50S RIBOSOMAL PROTEIN L33 (chains 1)
MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV

Sequence of entity 2 (2), FASTA

>2ZJP_2 50S RIBOSOMAL PROTEIN L34 (chains 2)
MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSDE

Sequence of entity 3 (3), FASTA

>2ZJP_3 50S RIBOSOMAL PROTEIN L35 (chains 3)
MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL
MLPRGK

Sequence of entity 4 (4), FASTA

>2ZJP_4 50S RIBOSOMAL PROTEIN L36 (chains 4)
MKVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQG

Sequence of entity 5 (5), FASTA

>2ZJP_5 NOSIHEPTIDE (chains 5)
SCTTCECCCSCSX

Sequence of entity 6 (A), FASTA

>2ZJP_6 50S RIBOSOMAL PROTEIN L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK

Sequence of entity 7 (B), FASTA

>2ZJP_7 50S RIBOSOMAL PROTEIN L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK

Sequence of entity 8 (C), FASTA

>2ZJP_8 50S RIBOSOMAL PROTEIN L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ

Sequence of entity 9 (D), FASTA

>2ZJP_9 50S RIBOSOMAL PROTEIN L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ

Sequence of entity 10 (E), FASTA

>2ZJP_10 50S RIBOSOMAL PROTEIN L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK

Sequence of entity 11 (F), FASTA

>2ZJP_11 50S RIBOSOMAL PROTEIN L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA

Sequence of entity 12 (G), FASTA

>2ZJP_12 50S RIBOSOMAL PROTEIN L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	35
NO1	4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid	C11 H11 N O3	1

Primary citation

Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin. Harms, J.M., Wilson, D.N., Schluenzen, F. et al. Mol Cell (2008) 30:26. DOI 10.1016/J.MOLCEL.2008.01.009 · PubMed

Other PDB entries of the same protein (UniProt Q9RSS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DM6 2.9 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans
2ZJR 2.91 Å, Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans
5DM7 3.0 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex…
1NKW 3.1 Å, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
4IO9 3.2 Å, Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus…
4IOA 3.2 Å, Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus…
7A0S 3.22 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
3PIO 3.25 Å, Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in…
1NWY 3.3 Å, Complex of the large ribosomal subunit from deinococcus radiodurans with azithromycin
2ZJQ 3.3 Å, Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans…
3CF5 3.3 Å, Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus…
7A0R 3.3 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I

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