7A0S: 50S ribosomal protein L2

Name: PDB 7A0S: 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
Published: 2021-08-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: antibiotic

50S Deinococcus radiodurans ribosome bounded with mycinamicin I. Determined by X-ray diffraction at 3.22 Å resolution. Released 18 Aug 2021.

Method: X-ray diffraction
Resolution: 3.22 Å
Organism: Deinococcus radiodurans R1
Chains: 28
Atoms: 84,486
Mol. weight: 1337.47 kDa
Ligands: QU2, MG, SPD, EOH
Released: 18 Aug 2021

Explore 7A0S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A0S contains 102 α-helices and 206 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, 3 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	74
β-strand	37-40	4	74
β-strand	48-51	4	74

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-14	6
α-helix	18-21	4
α-helix	25-37	13

Chain 3: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	37
β-strand	15	1	1
β-strand	23	1	1
α-helix	38-41	4
α-helix	53-59	7

Chain A: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	2
β-strand	17-19	3	2
α-helix	28-30	3
α-helix	31-33	3
β-strand	44	1	3
β-strand	49	1	3
β-strand	54	1	4
β-strand	65	1	5
β-strand	76-83	8	5
β-strand	92-97	6	5
β-strand	102-106	5	5
α-helix	107	1
β-strand	108	1	6
α-helix	111-112	2
β-strand	116-118	3	5
β-strand	119	1	7
β-strand	130-132	3	7
α-helix	133-135	3
α-helix	137	1
β-strand	141-143	3	7
β-strand	145	1	8
β-strand	155	1	8
β-strand	163-168	6	7
β-strand	172-176	5	7
β-strand	181	1	9
β-strand	182-186	5	7
β-strand	190-193	4	7
β-strand	196	1	6
α-helix	211-214	4
β-strand	217	1	4
α-helix	223-225	3
β-strand	271	1	9

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	10
β-strand	15-16	2	11
β-strand	19-20	2	11
β-strand	23-27	5	10
β-strand	31-32	2	12
β-strand	33-37	5	13
α-helix	39-42	4
β-strand	46-50	5	13
β-strand	53	1	14
α-helix	56-58	3
α-helix	61-70	10
β-strand	75	1	14
β-strand	78-82	5	13
β-strand	89-90	2	12
α-helix	92-95	4
β-strand	101-107	7	10
α-helix	108-110	3
β-strand	113-114	2	15
α-helix	116-120	5
β-strand	158-159	2	15
β-strand	164-171	8	10
β-strand	174-176	3	10
β-strand	181-185	5	10
β-strand	195-200	6	10

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-37	14
β-strand	47	1	16
β-strand	82	1	16
α-helix	97-110	14
β-strand	117	1	17
α-helix	130-138	9
β-strand	148-150	3	17
β-strand	152	1	18
α-helix	155-158	4
α-helix	159-161	3
β-strand	167-168	2	17
β-strand	171	1	18
α-helix	179-182	4
β-strand	185-187	3	17
α-helix	191-194	4

Chain D: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	25-27	3
β-strand	31-37	7	19
α-helix	40-43	4
α-helix	50-61	12
α-helix	64-65	2
β-strand	66-69	4	19
β-strand	84-91	8	19
α-helix	94-102	9
α-helix	103-107	5
β-strand	117	1	20
β-strand	128-131	4	19
β-strand	153-158	6	19
α-helix	163-166	4
α-helix	171-173	3
β-strand	177	1	20

Chain E: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	21
β-strand	25	1	22
β-strand	26-27	2	21
β-strand	34	1	22
β-strand	42	1	23
β-strand	45	1	24
β-strand	50	1	24
β-strand	53	1	23
α-helix	59-81	23
β-strand	83-90	8	25
β-strand	95-99	5	26
β-strand	102-106	5	26
β-strand	113-115	3	26
α-helix	116-118	3
β-strand	121-127	7	25
β-strand	130-135	6	25
α-helix	138-150	13
α-helix	153-155	3
β-strand	161-163	3	25

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 (2732-mer)	X	RNA	2880	Deinococcus radiodurans R1
RNA (122-mer)	Y	RNA	123	Deinococcus radiodurans R1
50S ribosomal protein L2	A	protein	274	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	205	Deinococcus radiodurans R1	Q9RXK1 (AlphaFold model)
50S ribosomal protein L5	D	protein	177	Deinococcus radiodurans R1	Q9RXJ0 (AlphaFold model)
50S ribosomal protein L6	E	protein	171	Deinococcus radiodurans R1	Q9RSL3
50S ribosomal protein L13	G	protein	143	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	136	Deinococcus radiodurans R1	Q9RXJ5
50S ribosomal protein L17	K	protein	116	Deinococcus radiodurans R1	Q9RSJ5

16 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>7A0S_1 RNA (2732-MER) (chains X)
GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGA
UUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGG
GGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUC
AGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAU
CAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCC
CUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGA
GCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGC
GCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGG
AAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAG
CAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAG
ACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGG
CGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAA
CCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUU
GUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUU
GAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUA
CCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCU
GCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUA
AAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGA
AGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAA
UGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUG
GUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
GUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACA
AGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAAC
GGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGG
ACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAU
CGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGA
AGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUAC
CGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUU
AAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGG
GGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAA
CAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAA
GCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAA
AUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCA
ACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGA
AAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGA
UAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCAC
CCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUA
GUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGA
CGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACAC
GUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCG
AUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCG
GCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCA
AGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGAC
AGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAG
AGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGU
AGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUG
AGUUCUCCCACUGUUUAUAAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGC
GUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Sequence of entity 2 (Y), FASTA

>7A0S_2 RNA (122-MER) (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU

Sequence of entity 3 (A), FASTA

>7A0S_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK

Sequence of entity 4 (B), FASTA

>7A0S_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASA

Sequence of entity 5 (C), FASTA

>7A0S_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ

Sequence of entity 6 (D), FASTA

>7A0S_6 50S ribosomal protein L5 (chains D)
QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITL
QKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAF
DGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK

Sequence of entity 7 (E), FASTA

>7A0S_7 50S ribosomal protein L6 (chains E)
GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRAL
HGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFA
VPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK

Sequence of entity 8 (G), FASTA

>7A0S_8 50S ribosomal protein L13 (chains G)
KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVA
LTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLK
VYAGETHPHSAQKPQVLKTQPLE

Sequence of entity 9 (H), FASTA

>7A0S_9 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 10 (I), FASTA

>7A0S_10 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAG

Sequence of entity 11 (J), FASTA

>7A0S_11 50S ribosomal protein L16 (chains J)
KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKI
YIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHK
LPIQTKMVKREVYDEA

Sequence of entity 12 (K), FASTA

>7A0S_12 50S ribosomal protein L17 (chains K)
MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL
HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV

Ligands and cofactors

ID	Name	Formula	Copies
QU2	mycinamicin I	C37 H61 N O12	1
MG	Magnesium ion	Mg	367
SPD	Spermidine	C7 H19 N3	8
EOH	Ethanol	C2 H6 O	1
CA	Calcium ion	Ca	5

Water and common crystallization additives (MPD, NA, K) are not listed.

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…
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
7A18 3.4 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV

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