7A0R: 50S ribosomal protein L2

Name: PDB 7A0R: 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 3.3 Å resolution. Released 18 Aug 2021.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Deinococcus radiodurans R1
Chains: 28
Atoms: 84,973
Mol. weight: 1323.96 kDa
Ligands: MG, QTZ
Released: 18 Aug 2021

Explore 7A0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A0R contains 103 α-helices and 182 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: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	62
β-strand	15-16	2	63
β-strand	22	1	63
β-strand	25	1	62
α-helix	35	1
β-strand	36-40	5	63
β-strand	48-52	5	63

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-14	6
α-helix	18-23	6
α-helix	25-37	13

Chain 3: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	12	1	31
β-strand	16	1	1
α-helix	18-20	3
α-helix	21	1
β-strand	22	1	1
α-helix	23	1
α-helix	38-42	5
α-helix	53-59	7

Chain A: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	2
β-strand	18-19	2	2
β-strand	54	1	3
β-strand	65	1	4
β-strand	77-83	7	4
β-strand	92-97	6	4
β-strand	102-106	5	4
β-strand	108	1	5
β-strand	116-117	2	4
β-strand	119	1	6
β-strand	130-132	3	6
α-helix	133-135	3
α-helix	137	1
β-strand	141-143	3	6
β-strand	146-148	3	7
β-strand	150-153	4	7
β-strand	163-165	3	6
β-strand	172-176	5	6
β-strand	182-186	5	6
β-strand	190-193	4	6
β-strand	196	1	5
α-helix	199-203	5
α-helix	209-214	6
β-strand	217	1	3
α-helix	223-225	3
α-helix	263-266	4

Chain B: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-16	14	8
β-strand	19-27	9	8
β-strand	31	1	9
β-strand	33-37	5	10
α-helix	39-42	4
β-strand	46-50	5	10
β-strand	53	1	11
α-helix	56-58	3
α-helix	61-70	10
β-strand	75	1	11
β-strand	78-82	5	10
β-strand	90	1	9
β-strand	101-107	7	8
β-strand	113-114	2	12
α-helix	116-120	5
β-strand	158-159	2	12
β-strand	164-176	13	8
β-strand	181-185	5	8
β-strand	195-200	6	8

Chain C: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	25-37	13
α-helix	49-51	3
α-helix	97-112	16
β-strand	116-119	4	13
α-helix	130-139	10
β-strand	149-151	3	13
α-helix	155-158	4
β-strand	168-170	3	13
α-helix	177-181	5
β-strand	186-189	4	13
α-helix	190-193	4

Chain D: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
α-helix	25-27	3
β-strand	33-36	4	14
α-helix	47-61	15
α-helix	64-65	2
β-strand	66	1	15
β-strand	69	1	16
β-strand	75	1	17
β-strand	78	1	17
β-strand	84	1	16
β-strand	88	1	15
β-strand	89-91	3	14
α-helix	94-102	9
α-helix	103-107	5
β-strand	129-130	2	18
β-strand	154-155	2	18
β-strand	156-157	2	14
α-helix	163-173	11

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	25-28	4	19
β-strand	31-34	4	19
α-helix	42-45	4
α-helix	59-80	22
β-strand	83-90	8	20
β-strand	95-99	5	21
β-strand	102-106	5	21
β-strand	113-115	3	21
β-strand	122-124	3	20
β-strand	130-135	6	20
α-helix	138-150	13
α-helix	153-155	3
β-strand	161-163	3	20

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 (2730-mer)	X	RNA	2877	Deinococcus radiodurans R1
RNA (120-mer)	Y	RNA	120	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	197	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

>7A0R_1 RNA (2730-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
AGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGC
GUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCA

Sequence of entity 2 (Y), FASTA

>7A0R_2 RNA (120-MER) (chains Y)
ACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAAC
ACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGU

Sequence of entity 3 (A), FASTA

>7A0R_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVT

Sequence of entity 4 (B), FASTA

>7A0R_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASA

Sequence of entity 5 (C), FASTA

>7A0R_5 50S ribosomal protein L4 (chains C)
AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQ
KGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVD
GFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDIL
RHDRLVIDAAALEIVEE

Sequence of entity 6 (D), FASTA

>7A0R_6 50S ribosomal protein L5 (chains D)
QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITL
QKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAF
DGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK

Sequence of entity 7 (E), FASTA

>7A0R_7 50S ribosomal protein L6 (chains E)
GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRAL
HGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFA
VPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK

Sequence of entity 8 (G), FASTA

>7A0R_8 50S ribosomal protein L13 (chains G)
KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVA
LTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLK
VYAGETHPHSAQKPQVLKTQPLE

Sequence of entity 9 (H), FASTA

>7A0R_9 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 10 (I), FASTA

>7A0R_10 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAG

Sequence of entity 11 (J), FASTA

>7A0R_11 50S ribosomal protein L16 (chains J)
KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKI
YIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHK
LPIQTKMVKREVYDEA

Sequence of entity 12 (K), FASTA

>7A0R_12 50S ribosomal protein L17 (chains K)
MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL
HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	345
QTZ	mycinamicin II	C37 H61 N O13	1

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

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