8BN3: Yeast 80S, ES7s delta, eIF5A, Stm1 containing

Name: PDB 8BN3: Yeast 80S, ES7s delta, eIF5A, Stm1 containing
Published: 2024-01-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Yeast 80S, ES7s delta, eIF5A, Stm1 containing. Determined by electron microscopy at 2.4 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae
Chains: 81
Atoms: 201,671
Mol. weight: 2979.33 kDa
Ligands: ZN, SPD, 3HE, MG
Released: 10 Jan 2024

Explore 8BN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BN3 contains 550 α-helices and 556 β-strands across 77 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 B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	19-23	5
α-helix	29-30	2
β-strand	31-38	8	1
β-strand	50-54	5	2
β-strand	65-68	4	3
α-helix	71-79	9
β-strand	83-85	3	3
α-helix	89-92	4
α-helix	97-106	10
β-strand	109-113	5	3
α-helix	119-123	5
α-helix	126-131	6
α-helix	134-135	2
β-strand	136-138	3	3
α-helix	144-152	9
β-strand	154-158	5	2
β-strand	164-171	8	1
α-helix	176-191	16
α-helix	197-199	3
β-strand	201-208	8	1
β-strand	213-215	3	1

Chain C0: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-24	5	27
α-helix	39-50	12
β-strand	55-60	6	27
β-strand	63-68	6	27
α-helix	70-80	11
α-helix	89-91	3

Chain C1: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	39	1	159
β-strand	42	1	159
α-helix	43-45	3
α-helix	46-50	5
β-strand	70-77	8	160
β-strand	83-94	12	160
β-strand	99-110	12	160
β-strand	122-127	6	160
β-strand	137-142	6	160

Chain C3: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	30-42	13
α-helix	47-56	10
α-helix	63-66	4
α-helix	71-78	8
α-helix	86-104	19
α-helix	109-132	24
α-helix	147-150	4

Chain C4: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	33
β-strand	26-31	6	33
β-strand	38-43	6	33
α-helix	44-46	3
α-helix	51-53	3
α-helix	57-74	18
β-strand	78-84	7	33
α-helix	94-95	2
α-helix	97-107	11
α-helix	110	1
β-strand	111-117	7	33
α-helix	126-128	3

Chain C5: 11 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
α-helix	30-36	7
α-helix	39-46	8
α-helix	51-65	15
α-helix	68	1
α-helix	72-75	4
β-strand	76-78	3	38
α-helix	83	1
β-strand	84	1	39
α-helix	85	1
α-helix	87-89	3
β-strand	93-97	5	38
β-strand	102-106	5	38
α-helix	109-111	3
β-strand	115	1	39
α-helix	116-119	4

Chain C6: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	168
β-strand	19-21	3	169
β-strand	22-23	2	168
β-strand	24	1	170
β-strand	29-31	3	169
β-strand	34	1	169
α-helix	43-45	3
α-helix	46-53	8
β-strand	63	1	170
β-strand	65-68	4	169
α-helix	74-96	23
α-helix	99-110	12
α-helix	123-127	5
α-helix	138-140	3

Chain C7: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	28-38	11
β-strand	39	1	123
α-helix	45-63	19
β-strand	101	1	175
α-helix	104-112	9
β-strand	120	1	175

69 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
60S ribosomal protein L1-A	B	protein	217	Saccharomyces cerevisiae	P0CX43 (AlphaFold model)
Rps5p	S5	protein	206	Saccharomyces cerevisiae	P26783 (AlphaFold model)
Small ribosomal subunit protein eS10A	C0	protein	96	Saccharomyces cerevisiae	Q08745 (AlphaFold model)
40S ribosomal protein S14-B	C4	protein	127	Saccharomyces cerevisiae	P39516 (AlphaFold model)
RPS15 isoform 1	C5	protein	124	Saccharomyces cerevisiae	Q01855
40S ribosomal protein S18-A	C8	protein	145	Saccharomyces cerevisiae	P0CX55
RPS20 isoform 1	D0	protein	107	Saccharomyces cerevisiae	P38701
40S ribosomal protein S25	D5	protein	70	Saccharomyces cerevisiae	Q3E792
RPS28A isoform 1	D8	protein	63	Saccharomyces cerevisiae	Q3E7X9
60S ribosomal protein L41-A	P	protein	15	Saccharomyces cerevisiae	P0CX86
5S ribosomal RNA	3	RNA	121	Saccharomyces cerevisiae
5.8S ribosomal RNA	4	RNA	158	Saccharomyces cerevisiae

69 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>8BN3_1 60S ribosomal protein L1-A (chains B)
MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPR
PNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQV
PRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLV
NQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY

Sequence of entity 2 (S5), FASTA

>8BN3_2 Rps5p (chains S5)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 3 (C0), FASTA

>8BN3_3 Small ribosomal subunit protein eS10A (chains C0)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPATYIQERN

Sequence of entity 4 (C4), FASTA

>8BN3_4 40S ribosomal protein S14-B (chains C4)
SQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAK
CKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSDSTRKKG
GRRGRRL

Sequence of entity 5 (C5), FASTA

>8BN3_5 RPS15 isoform 1 (chains C5)
KKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAA
PENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVR
HGRA

Sequence of entity 6 (C8), FASTA

>8BN3_6 40S ribosomal protein S18-A (chains C8)
SLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGEL
TQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRA
HRGIRHFWGLRVRGQHTKTTGRRRA

Sequence of entity 7 (D0), FASTA

>8BN3_7 RPS20 isoform 1 (chains D0)
QQQQIIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNGE
GSKTWETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVASN

Sequence of entity 8 (D5), FASTA

>8BN3_8 40S ribosomal protein S25 (chains D5)
AQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKH
SKQAIYTRAT

Sequence of entity 9 (D8), FASTA

>8BN3_9 RPS28A isoform 1 (chains D8)
TPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESEREAR
RLR

Sequence of entity 10 (P), FASTA

>8BN3_10 60S ribosomal protein L41-A (chains P)
MRARWRKKRTRRLKR

Sequence of entity 11 (3), FASTA

>8BN3_11 5S ribosomal RNA (chains 3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 12 (4), FASTA

>8BN3_12 5.8S ribosomal RNA (chains 4)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
SPD	Spermidine	C7 H19 N3	3
3HE	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2…	C15 H23 N O4	1
MG	Magnesium ion	Mg	220

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

Primary citation

Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Rauscher, R., Eggers, C., Dimitrova-Paternoga, L. et al. Nucleic Acids Res (2024) 52:4021-4036. DOI 10.1093/nar/gkae067 · PubMed

Other PDB entries of the same protein (UniProt P0CX43 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8AGX 2.4 Å, Yeast RQC complex in state with the RING domain of Ltn1 in the IN position
8T2X 2.46 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger…
9DOV 2.49 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8AAF 2.5 Å, Yeast RQC complex in state G
8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
9T3L 2.55 Å, Crystal structure of the Acl1 ankyrin repeat domain in complex with the second Rpl1 domain
8AGT 2.6 Å, Yeast RQC complex in state F
8AGV 2.6 Å, Yeast RQC complex in state H
8AGW 2.6 Å, Yeast RQC complex in state D
8AGZ 2.6 Å, Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position

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