2ZJR: 50S ribosomal protein L2

Name: PDB 2ZJR: Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans
Published: 2008-06-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans. Determined by X-ray diffraction at 2.91 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Deinococcus radiodurans
Chains: 30
Atoms: 83,819
Mol. weight: 1365.29 kDa
Ligands: MG
Released: 17 Jun 2008

Explore 2ZJR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZJR contains 86 α-helices and 183 β-strands across 25 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 4: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	10
β-strand	17-18	2	10
β-strand	23-25	3	10
β-strand	34-35	2	10

Chain A: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	37	1
β-strand	38	1	1
α-helix	39	1
β-strand	44	1	2
β-strand	49	1	2
β-strand	61	1	1
β-strand	65	1	3
β-strand	76-83	8	3
β-strand	92-97	6	3
β-strand	102-106	5	3
β-strand	108	1	4
β-strand	116-118	3	3
β-strand	119	1	5
β-strand	130	1	5
α-helix	133-135	3
β-strand	141-143	3	5
β-strand	161	1	4
β-strand	163-165	3	5
β-strand	172-177	6	5
β-strand	181-186	6	5
β-strand	192-194	3	5
β-strand	196	1	4
α-helix	212-214	3
α-helix	223-225	3
β-strand	267-268	2	5

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-16	14	6
β-strand	19-27	9	6
β-strand	31-32	2	7
β-strand	33-37	5	8
β-strand	46-50	5	8
α-helix	56-58	3
α-helix	61-68	8
β-strand	78-81	4	8
β-strand	89-90	2	7
β-strand	101-107	7	6
β-strand	110-114	5	9
α-helix	116-120	5
β-strand	158-161	4	9
β-strand	164-176	13	6
β-strand	181-185	5	6
β-strand	195-200	6	6

Chain C: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	24-38	15
α-helix	97-113	17
β-strand	118	1	11
α-helix	131-139	9
β-strand	148-151	4	12
α-helix	155-158	4
β-strand	167-170	4	12
α-helix	171-173	3
α-helix	177-182	6
β-strand	185-187	3	12
β-strand	189	1	11

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
α-helix	8-12	5
α-helix	13-17	5
β-strand	33-35	3	13
β-strand	37	1	14
α-helix	49-61	13
β-strand	66	1	15
β-strand	88	1	15
β-strand	90-91	2	13
α-helix	94-102	9
α-helix	103-107	5
β-strand	129-130	2	16
α-helix	143-145	3
β-strand	153	1	14
β-strand	154-155	2	16
β-strand	156-157	2	13
α-helix	163-172	10

Chain E: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	17
β-strand	17-18	2	18
β-strand	25-26	2	18
β-strand	44	1	19
β-strand	50	1	17
β-strand	51	1	19
α-helix	60-81	22
β-strand	83-88	6	20
β-strand	90	1	21
β-strand	99	1	22
β-strand	102	1	22
β-strand	104	1	23
β-strand	114	1	23
β-strand	121-124	4	20
β-strand	130-135	6	20
α-helix	138-151	14
α-helix	153-155	3
β-strand	161	1	21

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	75-78	4
α-helix	79-83	5
β-strand	97-99	3	24
α-helix	101-111	11
α-helix	112-114	3
α-helix	121-132	12
β-strand	136-138	3	24
α-helix	139	1

Chain G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	25
β-strand	50	1	26
α-helix	51-63	13
β-strand	79-83	5	25
β-strand	89	1	26
β-strand	99-102	4	27
β-strand	112-115	4	27
α-helix	123-131	9
α-helix	132-134	3
α-helix	139-145	7
β-strand	149-150	2	25
α-helix	156-159	4

17 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
ribosomal 5S RNA	Y	RNA	123	Deinococcus radiodurans
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	142	Deinococcus radiodurans	Q9RXJ5

18 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>2ZJR_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

>2ZJR_2 ribosomal 5S RNA (chains Y)
ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAA
ACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGG
GUU

Sequence of entity 3 (A), FASTA

>2ZJR_3 50S ribosomal protein L2 (chains A)
AVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRL
YRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGP
EAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGE
LRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTG
AGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK

Sequence of entity 4 (B), FASTA

>2ZJR_4 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK

Sequence of entity 5 (C), FASTA

>2ZJR_5 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ

Sequence of entity 6 (D), FASTA

>2ZJR_6 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ

Sequence of entity 7 (E), FASTA

>2ZJR_7 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK

Sequence of entity 8 (F), FASTA

>2ZJR_8 50S ribosomal protein L11 (chains F)
MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIY
ADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSV
EAAANTVAGTARSMGVTVEGGPNA

Sequence of entity 9 (G), FASTA

>2ZJR_9 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK

Sequence of entity 10 (H), FASTA

>2ZJR_10 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL

Sequence of entity 11 (I), FASTA

>2ZJR_11 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE

Sequence of entity 12 (J), FASTA

>2ZJR_12 50S ribosomal protein L16 (chains J)
MMLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFR
RGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFR
LAGHKLPIQTKMVKREVYDEAQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	35

Primary citation

Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Harms, J.M., Wilson, D.N., Schluenzen, F. et al. Mol Cell (2008) 30:26-38. DOI 10.1016/j.molcel.2008.01.009 · 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
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
7A18 3.4 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV

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