7A18: 50S ribosomal protein L2

Name: PDB 7A18: 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV
Published: 2021-10-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: antibiotic

50S Deinococcus radiodurans ribosome bounded with mycinamicin IV. Determined by X-ray diffraction at 3.4 Å resolution. Released 6 Oct 2021.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Deinococcus radiodurans R1
Chains: 28
Atoms: 84,387
Mol. weight: 1265.05 kDa
Ligands: MIV, SPD, MG
Released: 6 Oct 2021

Explore 7A18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A18 contains 100 α-helices and 176 β-strands across 26 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 1: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	61
β-strand	15-16	2	62
β-strand	22	1	62
β-strand	25-26	2	61
β-strand	37-40	4	62
β-strand	48-51	4	62

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-14	6
α-helix	18-22	5
α-helix	25-37	13

Chain 3: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	12	1	27
β-strand	15	1	1
β-strand	23-24	2	1
α-helix	38-41	4
β-strand	47-48	2	1
α-helix	53-59	7

Chain A: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	2
β-strand	18	1	2
β-strand	54	1	3
β-strand	76-83	8	4
β-strand	92-97	6	4
β-strand	102-106	5	4
α-helix	107	1
β-strand	108	1	5
β-strand	116-118	3	4
β-strand	130-132	3	6
α-helix	137	1
β-strand	141-143	3	6
β-strand	145-146	2	7
β-strand	153-155	3	7
β-strand	163-168	6	6
β-strand	173-176	4	6
β-strand	182-185	4	6
β-strand	190-193	4	6
β-strand	196	1	5
α-helix	209-213	5
β-strand	217	1	3
α-helix	262-266	5
β-strand	267	1	6

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-16	14	8
β-strand	19-27	9	8
β-strand	31-32	2	9
β-strand	33-37	5	10
α-helix	39-42	4
β-strand	46-53	8	10
α-helix	56-58	3
α-helix	61-70	10
β-strand	75-82	8	10
β-strand	89-90	2	9
α-helix	92-95	4
β-strand	101-107	7	8
α-helix	108-109	2
β-strand	113-114	2	11
α-helix	116-119	4
β-strand	158-159	2	11
β-strand	164-176	13	8
β-strand	181-185	5	8
β-strand	195-200	6	8

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-22	2
α-helix	27-38	12
α-helix	97-112	16
β-strand	116-118	3	12
α-helix	130-139	10
β-strand	148-151	4	12
α-helix	155-161	7
β-strand	167-169	3	12
α-helix	177-182	6
β-strand	186-188	3	12

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-19	17
β-strand	31-37	7	13
α-helix	47-61	15
α-helix	65	1
β-strand	66-69	4	14
β-strand	84-88	5	14
β-strand	89-91	3	13
α-helix	94-104	11
α-helix	117-119	3
β-strand	128-132	5	13
β-strand	152-158	7	13
α-helix	164-167	4
α-helix	168-171	4

Chain E: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	15
β-strand	26-27	2	15
β-strand	42-45	4	16
β-strand	50-53	4	16
α-helix	59-80	22
β-strand	83-90	8	17
β-strand	95-99	5	18
β-strand	102-106	5	18
β-strand	113-115	3	18
α-helix	116-118	3
β-strand	122-127	6	17
β-strand	130-135	6	17
α-helix	138-149	12
α-helix	150-152	3
α-helix	153-155	3
β-strand	161-164	4	17

18 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
RNA (2699-mer)	X	RNA	2699	Deinococcus radiodurans R1
RNA (122-mer)	Y	RNA	122	Deinococcus radiodurans R1
50S ribosomal protein L2	A	protein	271	Deinococcus radiodurans R1	Q9RXJ9 (AlphaFold model)
50S ribosomal protein L3	B	protein	206	Deinococcus radiodurans R1	Q9RXK2 (AlphaFold model)
50S ribosomal protein L4	C	protein	195	Deinococcus radiodurans R1	Q9RXK1 (AlphaFold model)
50S ribosomal protein L5	D	protein	176	Deinococcus radiodurans R1	Q9RXJ0 (AlphaFold model)
50S ribosomal protein L6	E	protein	171	Deinococcus radiodurans R1	Q9RSL3
50S ribosomal protein L13	G	protein	142	Deinococcus radiodurans R1	Q9RXY1
50S ribosomal protein L14	H	protein	134	Deinococcus radiodurans R1	Q9RXJ2
50S ribosomal protein L15	I	protein	137	Deinococcus radiodurans R1	Q9RSK9
50S ribosomal protein L16	J	protein	134	Deinococcus radiodurans R1	Q9RXJ5
50S ribosomal protein L17	K	protein	115	Deinococcus radiodurans R1	Q9RSJ5

16 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>7A18_1 RNA (2699-MER) (chains X)
GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGA
UUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGG
GGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUC
AGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAU
CAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAUCAAGCCGAAGUGGCUGG
AAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCCCUGAGUAGGUCGUUGU
UCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGAC
CGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAG
AACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUA
UUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCG
GAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGU
GAGCUAAGCAUGACCAGGUUGAAACCCCCGGGGGCGGAGGACCGAACCGGUGCCUGCUGA
AACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAG
UUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUC
ACAAGGCUAAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUG
CGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAA
AUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAA
GCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAU
GAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGGAGUUGUCUGGUAGGGG
AGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGA
UGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUC
CUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAG
CCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUU
ACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCA
GAAAAUCUACCGGUCUGCCUCAGACGUAUCGGGAGCCGAAGUUGGAAACGCGACGGUGCC
AAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCC
GAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACC
CCGUAACUUCGGAAGAAGGGGUCCCCACGCUGCGUGGGGCGCAGUGAAUAGGCCCAGGCG
ACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACG
CCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGA
ACGGCGGCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGU
AACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGC
GGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGA
UUCGGGUUUCUAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUG
GCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCAC
CUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGA
CUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGG
GCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUC
CAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAA
GGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUC
GUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUA
GUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAU
GCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCC
CAAGAUGAGUUCUCCCACUGAAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAG
GCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCA

Sequence of entity 2 (Y), FASTA

>7A18_2 RNA (122-MER) (chains Y)
CACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAA
CACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGG
UU

Sequence of entity 3 (A), FASTA

>7A18_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVT

Sequence of entity 4 (B), FASTA

>7A18_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASA

Sequence of entity 5 (C), FASTA

>7A18_5 50S ribosomal protein L4 (chains C)
AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQ
KGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVD
GFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDIL
RHDRLVIDAAALEIV

Sequence of entity 6 (D), FASTA

>7A18_6 50S ribosomal protein L5 (chains D)
QQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALIT
LQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNA
FDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPF

Sequence of entity 7 (E), FASTA

>7A18_7 50S ribosomal protein L6 (chains E)
GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRAL
HGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFA
VPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK

Sequence of entity 8 (G), FASTA

>7A18_8 50S ribosomal protein L13 (chains G)
KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVA
LTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLK
VYAGETHPHSAQKPQVLKTQPL

Sequence of entity 9 (H), FASTA

>7A18_9 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 10 (I), FASTA

>7A18_10 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAG

Sequence of entity 11 (J), FASTA

>7A18_11 50S ribosomal protein L16 (chains J)
KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKI
YIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHK
LPIQTKMVKREVYD

Sequence of entity 12 (K), FASTA

>7A18_12 50S ribosomal protein L17 (chains K)
MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL
HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIEL

Ligands and cofactors

ID	Name	Formula	Copies
MIV	Mycinamicin IV	C37 H61 N O11	1
SPD	Spermidine	C7 H19 N3	7
MG	Magnesium ion	Mg	277

Primary citation

Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida. Breiner-Goldstein, E., Eyal, Z., Matzov, D. et al. Nucleic Acids Res (2021) 49:9560-9573. DOI 10.1093/nar/gkab684 · PubMed

Other PDB entries of the same protein (UniProt Q9RXJ9 (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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