6ELZ: 60S ribosomal protein L13-A

Name: PDB 6ELZ: State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Published: 2017-12-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Determined by electron microscopy at 3.3 Å resolution. Released 27 Dec 2017.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 54
Atoms: 134,887
Mol. weight: 2788.71 kDa
Ligands: ZN
Released: 27 Dec 2017

Explore 6ELZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ELZ contains 427 α-helices and 444 β-strands across 51 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 a: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	72-74	3	121
α-helix	87-91	5
β-strand	101-103	3	122
α-helix	104-107	4
β-strand	111-113	3	121
β-strand	124-127	4	122
β-strand	129-130	2	121
α-helix	132-141	10
β-strand	145-147	3	122

Chain A: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	26
β-strand	38	1	27
α-helix	43-55	13
β-strand	59-61	3	26
β-strand	65	1	27
α-helix	74-81	8
β-strand	85-90	6	26
β-strand	98-102	5	26
β-strand	110-113	4	26
β-strand	118	1	28
β-strand	130	1	29
β-strand	133	1	30
β-strand	136-138	3	31
α-helix	141-143	3
α-helix	147-158	12
β-strand	170	1	30
β-strand	175-182	8	31
β-strand	185-195	11	31
β-strand	210-221	12	31
β-strand	222-229	8	26
β-strand	232-237	6	26

Chain b: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	16-27	12
α-helix	39-67	29
α-helix	71-73	3
α-helix	76-85	10
α-helix	88-116	29
α-helix	122-141	20
α-helix	146-157	12
β-strand	168-174	7	71
α-helix	180-185	6
β-strand	206-210	5	71
β-strand	215-220	6	71
α-helix	234-245	12
β-strand	250-254	5	71
α-helix	259-261	3
α-helix	264-274	11
β-strand	284-287	4	71
α-helix	304-306	3
α-helix	309-311	3
β-strand	317-319	3	71
α-helix	327-341	15
α-helix	380-383	4
α-helix	385-387	3
α-helix	396-398	3
α-helix	399-405	7
α-helix	412-414	3
α-helix	425-427	3
β-strand	435-436	2	72
β-strand	439-440	2	72
α-helix	441-444	4
α-helix	449-464	16

Chain B: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	36	1	6
α-helix	40-41	2
β-strand	43	1	7
β-strand	45-47	3	8
β-strand	49-50	2	9
β-strand	54-60	7	9
β-strand	70-80	11	9
β-strand	84-95	12	10
β-strand	98-106	9	10
α-helix	112-117	6
α-helix	131-137	7
α-helix	144-153	10
β-strand	157-163	7	10
α-helix	176-177	2
β-strand	178-182	5	10
β-strand	183	1	7
β-strand	185	1	6
α-helix	188-196	9
β-strand	202-203	2	10
β-strand	214-221	8	8
β-strand	226-227	2	11
β-strand	268-269	2	11
β-strand	273-281	9	8
β-strand	282-285	4	9
α-helix	307	1
β-strand	321-325	5	9
β-strand	334	1	9
β-strand	337-339	3	8
α-helix	348-351	4
α-helix	353-354	2
β-strand	356-359	4	9
α-helix	373-380	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	23-25	3	73
α-helix	27-36	10
β-strand	41-44	4	73
α-helix	50-63	14
β-strand	66-69	4	73
α-helix	74-81	8
β-strand	89-92	4	73

Chain C: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	13
β-strand	15-20	6	13
α-helix	32-43	12
β-strand	62-63	2	14
β-strand	76-77	2	14
β-strand	88	1	14
α-helix	97-99	3
α-helix	115-127	13
α-helix	134-138	5
β-strand	150-152	3	13
α-helix	154-156	3
α-helix	162-172	11
α-helix	175-180	6
β-strand	186-187	2	15
β-strand	199-200	2	15
β-strand	206-209	4	13
α-helix	215-218	4
β-strand	226-229	4	13
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	13
α-helix	254-262	9
α-helix	276-279	4
α-helix	287-290	4
α-helix	293-298	6
α-helix	300-302	3
α-helix	321-326	6
α-helix	331-336	6
α-helix	350-352	3
α-helix	353-359	7

Chain d: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	76
β-strand	10	1	77
β-strand	12-15	4	76
α-helix	16-19	4
α-helix	25-27	3
α-helix	28-44	17
β-strand	48-51	4	76
α-helix	53-59	7
α-helix	60-62	3
β-strand	70-77	8	76
β-strand	90-95	6	76
β-strand	108	1	77
α-helix	109-111	3

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	268	1	55
β-strand	269	1	56
α-helix	275-286	12
β-strand	292-296	5	57
α-helix	302-311	10
β-strand	317-318	2	57
α-helix	325-336	12
β-strand	343-346	4	57
β-strand	360-363	4	57
α-helix	366-367	2
α-helix	372-377	6
β-strand	389-391	3	57
β-strand	393	1	56
β-strand	414	1	55
α-helix	427-433	7
α-helix	438-455	18
α-helix	468-474	7

43 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
25S ribosomal RNA	1	RNA	3396	Saccharomyces cerevisiae S288c
5.8S ribosomal RNA	2	RNA	158	Saccharomyces cerevisiae S288c
Internal transcribed spacer 2	6	RNA	232	Saccharomyces cerevisiae S288c
60S ribosomal protein L13-A	L	protein	199	Saccharomyces cerevisiae S288c	Q12690 (AlphaFold model)
60S ribosomal protein L15-A	N	protein	204	Saccharomyces cerevisiae S288c	P05748 (AlphaFold model)
60S ribosomal protein L18-A	Q	protein	186	Saccharomyces cerevisiae S288c	P0CX49 (AlphaFold model)
60S ribosomal protein L19-A	R	protein	189	Saccharomyces cerevisiae S288c	P0CX82 (AlphaFold model)
60S ribosomal protein L20-A	S	protein	172	Saccharomyces cerevisiae S288c	P0CX23
60S ribosomal protein L21-A	T	protein	160	Saccharomyces cerevisiae S288c	Q02753
60S ribosomal protein L22-A	U	protein	121	Saccharomyces cerevisiae S288c	P05749
60S ribosomal protein L27-A	Z	protein	136	Saccharomyces cerevisiae S288c	P0C2H6
60S ribosomal protein L30	c	protein	105	Saccharomyces cerevisiae S288c	P14120

42 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6ELZ_1 25S ribosomal RNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU

Sequence of entity 2 (2), FASTA

>6ELZ_2 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 3 (6), FASTA

>6ELZ_3 Internal transcribed spacer 2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA

Sequence of entity 4 (L), FASTA

>6ELZ_4 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Sequence of entity 5 (N), FASTA

>6ELZ_5 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK

Sequence of entity 6 (Q), FASTA

>6ELZ_6 60S ribosomal protein L18-A (chains Q)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Sequence of entity 7 (R), FASTA

>6ELZ_7 60S ribosomal protein L19-A (chains R)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 8 (S), FASTA

>6ELZ_8 60S ribosomal protein L20-A (chains S)
MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVS
INQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRS
IHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY

Sequence of entity 9 (T), FASTA

>6ELZ_9 60S ribosomal protein L21-A (chains T)
MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK
TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKCRQEFLERVKANAAKRAEAK
AQGVAVQLKRQPAQPRESRIVSTEGNVPQTLAPVPYETFI

Sequence of entity 10 (U), FASTA

>6ELZ_10 60S ribosomal protein L22-A (chains U)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E

Sequence of entity 11 (Z), FASTA

>6ELZ_11 60S ribosomal protein L27-A (chains Z)
MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK
KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE
RHQAGKNQWFFSKLRF

Sequence of entity 12 (c), FASTA

>6ELZ_12 60S ribosomal protein L30 (chains c)
MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYA
MLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Kater, L., Thoms, M., Barrio-Garcia, C. et al. Cell (2017) 171:1599-1610.e14. DOI 10.1016/j.cell.2017.11.039 · PubMed

Other PDB entries of the same protein (UniProt Q12690 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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