5JVG: 50S ribosomal protein L2

The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin. Determined by X-ray diffraction at 3.43 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 3.43 Å
Organisms: Deinococcus radiodurans R1, Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422), Deinococcus radiodurans
Chains: 29
Atoms: 85,766
Mol. weight: 1372.76 kDa
Ligands: SPD, MG, 6NO
Released: 9 Nov 2016

Explore 5JVG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JVG contains 94 α-helices and 176 β-strands across 27 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, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
β-strand	26-27	2	1
β-strand	37	1	2
β-strand	51	1	2

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	18-23	6
α-helix	25-35	11
α-helix	43-45	3

Chain 3: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	10
β-strand	22-24	3	10
α-helix	39-41	3
β-strand	47-48	2	10
α-helix	54-57	4

Chain A: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
β-strand	17	1	3
β-strand	76-78	3	4
β-strand	82-83	2	5
β-strand	92-93	2	5
β-strand	97	1	4
β-strand	105-106	2	5
β-strand	108	1	6
β-strand	116-118	3	4
β-strand	131-132	2	7
α-helix	133-135	3
α-helix	137	1
β-strand	141-143	3	8
β-strand	145-146	2	9
β-strand	153-155	3	9
β-strand	163-168	6	8
β-strand	172-176	5	8
β-strand	182-186	5	8
β-strand	190-191	2	7
β-strand	192-193	2	8
β-strand	196	1	6
α-helix	262-265	4
β-strand	268	1	8

Chain B: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-16	14	11
β-strand	19-27	9	11
β-strand	33-37	5	12
β-strand	46-50	5	12
β-strand	53	1	13
α-helix	61-69	9
β-strand	75	1	13
β-strand	78-82	5	12
β-strand	101	1	14
β-strand	102-107	6	11
β-strand	113-114	2	15
α-helix	116-119	4
β-strand	158-159	2	15
β-strand	164-167	4	11
β-strand	171	1	14
β-strand	172-176	5	11
β-strand	181-185	5	11
β-strand	195-200	6	11

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	24-38	15
α-helix	97-112	16
β-strand	117	1	16
α-helix	123-125	3
α-helix	131-139	9
β-strand	148-150	3	16
α-helix	155-159	5
β-strand	167-169	3	16
α-helix	177-182	6
β-strand	185-187	3	16

Chain D: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	13-17	5
β-strand	31-38	8	17
α-helix	50-61	12
α-helix	64-65	2
β-strand	66-67	2	17
β-strand	87-92	6	17
α-helix	94-102	9
α-helix	103-107	5
α-helix	108-110	3
β-strand	128-129	2	17
β-strand	153-158	6	17
α-helix	164-169	6

Chain E: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	18
β-strand	16-20	5	19
β-strand	23-27	5	19
β-strand	33-34	2	19
β-strand	42-45	4	18
β-strand	50-53	4	18
α-helix	65-78	14
β-strand	83-90	8	20
β-strand	95-99	5	21
β-strand	102-106	5	21
β-strand	113-115	3	21
α-helix	117-118	2
β-strand	121-127	7	20
β-strand	130-135	6	20
α-helix	138-150	13
α-helix	153-155	3
β-strand	161-164	4	20

19 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
23S ribosomal RNA	X	RNA	2877	Deinococcus radiodurans R1
5S ribosomal RNA	Y	RNA	124	Deinococcus radiodurans R1
50S ribosomal protein L2	A	protein	275	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXJ9 (AlphaFold model)
50S ribosomal protein L3	B	protein	211	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXK2 (AlphaFold model)
50S ribosomal protein L4	C	protein	205	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXK1 (AlphaFold model)
50S ribosomal protein L5	D	protein	180	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXJ0 (AlphaFold model)
50S ribosomal protein L6	E	protein	185	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RSL3
50S ribosomal protein L11	F	protein	144	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RSS7
50S ribosomal protein L13	G	protein	174	Deinococcus radiodurans	Q9RXY1
50S ribosomal protein L14	H	protein	134	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXJ2
50S ribosomal protein L15	I	protein	156	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RSK9
50S ribosomal protein L16	J	protein	141	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Q9RXJ5

17 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>5JVG_1 23S ribosomal 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
GCUGCGAAAUGAAGCCCCGGUGAACGGCGACCGUAACUAUAACGGUCCUAAGGUAGCGAA
AUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCA
ACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGA
AAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGA
UAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCAC
CCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUA
GUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGA
CGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACAC
GUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCG
AUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCG
GCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCA
AGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGAC
AGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAG
AGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGU
AGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUG
AGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGC
GUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCA

Sequence of entity 2 (Y), FASTA

>5JVG_2 5S ribosomal RNA (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUUU

Sequence of entity 3 (A), FASTA

>5JVG_3 50S ribosomal protein L2 (chains A)
MAVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKR
LYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAG
PEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSG
ELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRT
GAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK

Sequence of entity 4 (B), FASTA

>5JVG_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK

Sequence of entity 5 (C), FASTA

>5JVG_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ

Sequence of entity 6 (D), FASTA

>5JVG_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ

Sequence of entity 7 (E), FASTA

>5JVG_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK

Sequence of entity 8 (F), FASTA

>5JVG_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA

Sequence of entity 9 (G), FASTA

>5JVG_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK

Sequence of entity 10 (H), FASTA

>5JVG_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 11 (I), FASTA

>5JVG_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE

Sequence of entity 12 (J), FASTA

>5JVG_12 50S ribosomal protein L16 (chains J)
MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRR
GGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRL
AGHKLPIQTKMVKREVYDEAQ

Ligands and cofactors

ID	Name	Formula	Copies
SPD	Spermidine	C7 H19 N3	3
MG	Magnesium ion	Mg	446
6NO	Avilamycin	C61 H88 Cl2 O32	1

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

Primary citation

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding. Krupkin, M., Wekselman, I., Matzov, D. et al. Proc Natl Acad Sci U S A (2016) 113:E6796-E6805. DOI 10.1073/pnas.1614297113 · 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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