3PIO: 50S ribosomal protein L2

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit. Determined by X-ray diffraction at 3.25 Å resolution. Released 23 Feb 2011.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Deinococcus radiodurans R1, Deinococcus radiodurans
Chains: 30
Atoms: 84,383
Mol. weight: 1370.43 kDa
Ligands: MG, LMA
Released: 23 Feb 2011

Explore 3PIO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PIO contains 93 α-helices and 194 β-strands across 28 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, 5 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	1
β-strand	15-16	2	2
β-strand	25-26	2	1
β-strand	37-39	3	2
β-strand	49-51	3	2

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	18-22	5
α-helix	25-34	10

Chain 3: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	24	1	10
β-strand	47	1	10
α-helix	54-57	4

Chain 4: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	17
β-strand	15-18	4	18
β-strand	23-26	4	18
α-helix	30-32	3
β-strand	34	1	17
β-strand	35	1	18

Chain A: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	38	1	3
β-strand	45	1	4
β-strand	50	1	4
β-strand	63	1	3
β-strand	77-84	8	5
β-strand	93-98	6	5
β-strand	103	1	5
β-strand	106-107	2	5
β-strand	109	1	6
β-strand	117-119	3	5
β-strand	131-133	3	7
α-helix	134-136	3
α-helix	138	1
β-strand	143-144	2	7
β-strand	146	1	8
β-strand	156	1	8
β-strand	164	1	7
β-strand	166-169	4	9
β-strand	173-178	6	9
β-strand	182-187	6	9
β-strand	191-194	4	7
β-strand	197	1	6
α-helix	224-226	3
α-helix	263-266	4
β-strand	268-269	2	9

Chain B: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
β-strand	15-16	2	12
β-strand	19-20	2	12
β-strand	23-27	5	11
β-strand	31	1	13
β-strand	33-37	5	14
β-strand	46-50	5	14
β-strand	53	1	15
α-helix	56-58	3
α-helix	61-70	10
β-strand	75	1	15
β-strand	78-80	3	14
β-strand	90	1	13
β-strand	101-107	7	11
α-helix	108-109	2
β-strand	112-114	3	16
α-helix	116-119	4
β-strand	158-160	3	16
β-strand	164-176	13	11
β-strand	181-185	5	11
β-strand	195-200	6	11

Chain C: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	16-18	3
α-helix	24-36	13
α-helix	97-111	15
β-strand	116-117	2	19
α-helix	131-137	7
β-strand	148-150	3	19
α-helix	155-159	5
β-strand	169	1	19
α-helix	171-173	3
α-helix	177-182	6
β-strand	185-187	3	19

Chain D: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	13-15	3
β-strand	31-39	9	20
β-strand	41	1	21
β-strand	44	1	21
α-helix	48-60	13
α-helix	64-65	2
β-strand	66	1	20
β-strand	86-91	6	20
α-helix	94-102	9
α-helix	103-107	5
β-strand	117	1	22
β-strand	128-129	2	20
β-strand	134	1	23
α-helix	143-145	3
β-strand	151	1	23
β-strand	152-158	7	20
α-helix	164-174	11
β-strand	177	1	22

20 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
Ribosomal 23S RNA	X	RNA	2880	Deinococcus radiodurans R1
5S ribosomal RNA	Y	RNA	123	Deinococcus radiodurans R1
50S ribosomal protein L2	A	protein	274	Deinococcus radiodurans	Q9RXJ9 (AlphaFold model)
50S ribosomal protein L3	B	protein	211	Deinococcus radiodurans	Q9RXK2 (AlphaFold model)
50S ribosomal protein L4	C	protein	205	Deinococcus radiodurans	Q9RXK1 (AlphaFold model)
50S ribosomal protein L5	D	protein	180	Deinococcus radiodurans	Q9RXJ0 (AlphaFold model)
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
50S ribosomal protein L14	H	protein	134	Deinococcus radiodurans	Q9RXJ2
50S ribosomal protein L15	I	protein	156	Deinococcus radiodurans	Q9RSK9
50S ribosomal protein L16	J	protein	141	Deinococcus radiodurans	Q9RXJ5

18 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>3PIO_1 RIBOSOMAL 23S RNA (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
GUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Sequence of entity 2 (Y), FASTA

>3PIO_2 5S ribosomal RNA (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU

Sequence of entity 3 (A), FASTA

>3PIO_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK

Sequence of entity 4 (B), FASTA

>3PIO_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK

Sequence of entity 5 (C), FASTA

>3PIO_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ

Sequence of entity 6 (D), FASTA

>3PIO_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ

Sequence of entity 7 (E), FASTA

>3PIO_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK

Sequence of entity 8 (F), FASTA

>3PIO_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA

Sequence of entity 9 (G), FASTA

>3PIO_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK

Sequence of entity 10 (H), FASTA

>3PIO_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 11 (I), FASTA

>3PIO_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE

Sequence of entity 12 (J), FASTA

>3PIO_12 50S ribosomal protein L16 (chains J)
MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRR
GGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRL
AGHKLPIQTKMVKREVYDEAQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	154
LMA	Lankamycin	C43 H74 O15	1

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

Primary citation

Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Belousoff, M.J., Shapira, T., Bashan, A. et al. Proc Natl Acad Sci U S A (2011) 108:2717-2722. DOI 10.1073/pnas.1019406108 · 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
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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