6EM5: 60S ribosomal protein L13-A

Name: PDB 6EM5: State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes
Published: 2017-12-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Determined by electron microscopy at 4.3 Å resolution. Released 27 Dec 2017.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 57
Atoms: 74,285
Mol. weight: 2928.07 kDa
Released: 27 Dec 2017

Explore 6EM5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EM5 contains 458 α-helices and 486 β-strands across 54 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 3: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	18-20	3	122
β-strand	26-28	3	122
β-strand	37	1	122
β-strand	50-55	6	149
β-strand	60-65	6	149
α-helix	67-70	4
β-strand	77-81	5	149
α-helix	86-96	11
α-helix	102-116	15
α-helix	121-126	6
α-helix	141-144	4
α-helix	149-156	8
α-helix	158-170	13

Chain 4: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	15-30	16
α-helix	39-54	16
α-helix	59-75	17
α-helix	79-81	3
α-helix	95-109	15
α-helix	118-134	17
α-helix	143-154	12
α-helix	168-176	9
α-helix	214-226	13
α-helix	232-241	10

Chain 5: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-17	6	10
β-strand	22	1	11
β-strand	23	1	12
β-strand	30	1	11
β-strand	34-38	5	10
α-helix	43-45	3
β-strand	47-52	6	13
β-strand	57-62	6	13
β-strand	67-76	10	13
β-strand	104-114	11	13
α-helix	120-126	7
β-strand	140-145	6	14
β-strand	154-159	6	14
β-strand	163-169	7	14
β-strand	175-182	8	14
α-helix	184	1
α-helix	186-187	2
β-strand	189-192	4	15
β-strand	204-209	6	15
β-strand	212-219	8	15
α-helix	220	1
β-strand	226-231	6	15
α-helix	234-237	4
α-helix	242-245	4
β-strand	248-253	6	16
α-helix	255-257	3
α-helix	261-262	2
β-strand	269-274	6	16
β-strand	278-283	6	16
β-strand	292-295	4	16
α-helix	298-300	3
β-strand	303-309	7	17
β-strand	317	1	18
β-strand	323	1	18
β-strand	332-337	6	17
β-strand	342-345	4	17
β-strand	351	1	17
β-strand	366-370	5	12
β-strand	374-378	5	12
β-strand	383-388	6	12
β-strand	394-399	6	12
β-strand	404-411	8	10

Chain A: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	30
β-strand	38	1	31
α-helix	43-55	13
β-strand	59-61	3	30
β-strand	65	1	31
α-helix	74-81	8
β-strand	85-90	6	30
β-strand	98-102	5	30
β-strand	110-113	4	30
β-strand	118	1	32
β-strand	130	1	33
β-strand	133	1	34
β-strand	136-138	3	35
α-helix	141-143	3
α-helix	147-158	12
β-strand	170	1	34
β-strand	175-182	8	35
β-strand	185-195	11	35
β-strand	210-221	12	35
β-strand	222-229	8	30
β-strand	232-237	6	30

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	79
α-helix	180-185	6
β-strand	206-210	5	79
β-strand	215-220	6	79
α-helix	234-245	12
β-strand	250-254	5	79
α-helix	259-261	3
α-helix	264-274	11
β-strand	284-287	4	79
α-helix	304-306	3
α-helix	309-311	3
β-strand	317-319	3	79
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	80
β-strand	439-440	2	80
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	1
α-helix	40-41	2
β-strand	43	1	2
β-strand	45-47	3	3
β-strand	49-50	2	4
β-strand	54-60	7	4
β-strand	70-80	11	4
β-strand	84-95	12	5
β-strand	98-106	9	5
α-helix	112-117	6
α-helix	131-137	7
α-helix	144-153	10
β-strand	157-163	7	5
α-helix	176-177	2
β-strand	178-182	5	5
β-strand	183	1	2
β-strand	185	1	1
α-helix	188-196	9
β-strand	202-203	2	5
β-strand	214-221	8	3
β-strand	226-227	2	6
β-strand	268-269	2	6
β-strand	273-281	9	3
β-strand	282-285	4	4
α-helix	307	1
β-strand	321-325	5	4
β-strand	334	1	4
β-strand	337-339	3	3
α-helix	348-351	4
α-helix	353-354	2
β-strand	356-359	4	4
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	84
α-helix	27-36	10
β-strand	41-44	4	84
α-helix	50-63	14
β-strand	66-69	4	84
α-helix	74-81	8
β-strand	89-92	4	84

Chain C: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	7
β-strand	15-20	6	7
α-helix	32-43	12
β-strand	62-63	2	8
β-strand	76-77	2	8
β-strand	88	1	8
α-helix	97-99	3
α-helix	115-127	13
α-helix	134-138	5
β-strand	150-152	3	7
α-helix	154-156	3
α-helix	162-172	11
α-helix	175-180	6
β-strand	186-187	2	9
β-strand	199-200	2	9
β-strand	206-209	4	7
α-helix	215-218	4
β-strand	226-229	4	7
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	7
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

46 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
5.8S ribosomal RNA	2	RNA	158	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Internal Transcribed Spacer 2	6	RNA	232	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
60S ribosomal protein L13-A	L	protein	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12690 (AlphaFold model)
60S ribosomal protein L14-A	M	protein	138	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36105 (AlphaFold model)
60S ribosomal protein L15-A	N	protein	204	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05748 (AlphaFold model)
60S ribosomal protein L18-A	Q	protein	186	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX49 (AlphaFold model)
60S ribosomal protein L19-A	R	protein	189	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX82
60S ribosomal protein L20-A	S	protein	172	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX23
60S ribosomal protein L21-A	T	protein	160	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02753
60S ribosomal protein L22-A	U	protein	121	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05749
60S ribosomal protein L27-A	Z	protein	136	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0C2H6
60S ribosomal protein L30	c	protein	105	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14120

45 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6EM5_1 5.8S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 2 (6), FASTA

>6EM5_2 Internal Transcribed Spacer 2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUUUCAUUGGAUGUUUUUUUUCCAAAGAGAGGUUUCUCUGCGUGCUUGAGGUAUAA
UGCAAGUACGGUCGUUUUAGGUUUUACCAACUGCGGCUAAUCUUUUUUUAUACUGAGCGU
AUUGGAACGUUAUCGAUAAGAAGAGAGCGUCUAGGCGAACAAUGUUCUUAAA

Sequence of entity 3 (L), FASTA

>6EM5_3 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Sequence of entity 4 (M), FASTA

>6EM5_4 60S ribosomal protein L14-A (chains M)
MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINL
GQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQV
MVLRKQKRYTVKKALAKA

Sequence of entity 5 (N), FASTA

>6EM5_5 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK

Sequence of entity 6 (Q), FASTA

>6EM5_6 60S ribosomal protein L18-A (chains Q)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Sequence of entity 7 (R), FASTA

>6EM5_7 60S ribosomal protein L19-A (chains R)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 8 (S), FASTA

>6EM5_8 60S ribosomal protein L20-A (chains S)
MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVS
INQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRS
IHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY

Sequence of entity 9 (T), FASTA

>6EM5_9 60S ribosomal protein L21-A (chains T)
MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK
TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKCRQEFLERVKANAAKRAEAK
AQGVAVQLKRQPAQPRESRIVSTEGNVPQTLAPVPYETFI

Sequence of entity 10 (U), FASTA

>6EM5_10 60S ribosomal protein L22-A (chains U)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E

Sequence of entity 11 (Z), FASTA

>6EM5_11 60S ribosomal protein L27-A (chains Z)
MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK
KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE
RHQAGKNQWFFSKLRF

Sequence of entity 12 (c), FASTA

>6EM5_12 60S ribosomal protein L30 (chains c)
MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYA
MLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

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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