8CDR: 40S ribosomal protein S24-A

Name: PDB 8CDR: Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin
Published: 2023-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin. Determined by electron microscopy at 2.04 Å resolution. Released 20 Sept 2023.

Method: Electron microscopy
Resolution: 2.04 Å
Organisms: Saccharomyces cerevisiae, Escherichia coli
Chains: 84
Atoms: 207,753
Mol. weight: 3308.56 kDa
Ligands: ZN, MG, SPD, GDP
Released: 20 Sept 2023

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

Secondary structure: helices and β-sheets

8CDR contains 548 α-helices and 554 β-strands across 75 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 0: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
β-strand	9-15	7	1
β-strand	20-28	9	1
α-helix	37-47	11
β-strand	55-62	8	1
α-helix	63	1
β-strand	68-76	9	1
α-helix	79-85	7
α-helix	88-94	7
α-helix	98-100	3
α-helix	102-104	3
α-helix	105-117	13
α-helix	123-131	9

Chain 1: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
β-strand	60	1	7
α-helix	62-67	6
α-helix	76-85	10
β-strand	89-91	3	7
β-strand	101-103	3	7

Chain 2: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	17
β-strand	28	1	18
β-strand	29-31	3	17
β-strand	36-43	8	19
α-helix	50-56	7
β-strand	57	1	20
β-strand	66-73	8	19
α-helix	75-80	6

Chain 3: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-35	4	32
β-strand	44-47	4	32
α-helix	54	1
β-strand	55	1	33
α-helix	56	1
β-strand	62	1	33
β-strand	79-80	2	32

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-19	10	39
β-strand	25-32	8	39
β-strand	39-44	6	39
β-strand	52-54	3	39
α-helix	63-65	3

Chain 5: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	44
α-helix	33-35	3
β-strand	38-39	2	44
α-helix	40-45	6
β-strand	53	1	45

Chain 6: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	13-16	4
α-helix	21-23	3
α-helix	27-31	5
α-helix	33-44	12

Chain 7: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	53
β-strand	20-22	3	54
β-strand	32-37	6	54
β-strand	41-46	6	54
β-strand	56-60	5	54
β-strand	68-73	6	55
β-strand	80-84	5	55
β-strand	88-92	5	55
β-strand	99-104	6	55
β-strand	110	1	56
β-strand	114	1	57
β-strand	122-123	2	57
β-strand	126	1	56
β-strand	130	1	56
β-strand	133-134	2	57
β-strand	142	1	57
β-strand	179	1	58
β-strand	191	1	58
β-strand	201-204	4	59
β-strand	211-214	4	59
β-strand	220-221	2	60
β-strand	233-234	2	60
β-strand	240-245	6	61
β-strand	252-256	5	61
β-strand	259-263	5	61
β-strand	289-294	6	53
β-strand	300-305	6	53
β-strand	310-316	7	53

67 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
40S ribosomal protein S24-A	0	protein	135	Saccharomyces cerevisiae	P0CX31 (AlphaFold model)
40S ribosomal protein S25-A	1	protein	108	Saccharomyces cerevisiae	Q3E792 (AlphaFold model)
40S ribosomal protein S26	2	protein	119	Saccharomyces cerevisiae	P39938 (AlphaFold model)
40S ribosomal protein S27-A	3	protein	82	Saccharomyces cerevisiae	P35997 (AlphaFold model)
40S ribosomal protein S28-A	4	protein	67	Saccharomyces cerevisiae	Q3E7X9
HLJ1_G0030400.mRNA.1.CDS.1	5	protein	56	Saccharomyces cerevisiae	P41057
40S ribosomal protein S30-A	6	protein	63	Saccharomyces cerevisiae	P0CX33
Guanine nucleotide-binding protein subunit beta-like protein	7	protein	319	Saccharomyces cerevisiae	P38011
Ubiquitin-40S ribosomal protein S31	8	protein	152	Saccharomyces cerevisiae	P05759
60S ribosomal protein L16-A	A	protein	199	Saccharomyces cerevisiae	P26784
25S ribosomal RNA	AA	RNA	3396	Saccharomyces cerevisiae
Elongation factor 2	Aa	protein	842	Saccharomyces cerevisiae	P32324

72 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8CDR_1 40S ribosomal protein S24-A (chains 0)
MSDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGF
RTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKKIFG
TGKRLAKKVARRNAD

Sequence of entity 2 (1), FASTA

>8CDR_2 40S ribosomal protein S25-A (chains 1)
MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYV
SVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE

Sequence of entity 3 (2), FASTA

>8CDR_3 40S ribosomal protein S26 (chains 2)
MPKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYP
EYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPPQRPRFNRENKVSPADAAKKAL

Sequence of entity 4 (3), FASTA

>8CDR_4 40S ribosomal protein S27-A (chains 3)
MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCS
TILCTPTGGKAKLSEGTSFRRK

Sequence of entity 5 (4), FASTA

>8CDR_5 40S ribosomal protein S28-A (chains 4)
MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESE
REARRLR

Sequence of entity 6 (5), FASTA

>8CDR_6 HLJ1_G0030400.mRNA.1.CDS.1 (chains 5)
MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR

Sequence of entity 7 (6), FASTA

>8CDR_7 40S ribosomal protein S30-A (chains 6)
MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGP
SVQ

Sequence of entity 8 (7), FASTA

>8CDR_8 Guanine nucleotide-binding protein subunit beta-like protein (chains 7)
MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRS
FKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKAS
MIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKA
WNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEV
FSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQT
LFAGYTDNVIRVWQVMTAN

Sequence of entity 9 (8), FASTA

>8CDR_9 Ubiquitin-40S ribosomal protein S31 (chains 8)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGGKKRKKKVYTTPKKIKHKHKKVKLAVLSYYKVDAEGKVTKLRRE
CSNPTCGAGVFLANHKDRLYCGKCHSVYKVNA

Sequence of entity 10 (A), FASTA

>8CDR_10 60S ribosomal protein L16-A (chains A)
MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRK
ATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVV
PQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVAS
ANATAAESDVAKQLAALGY

Sequence of entity 11 (AA), FASTA

>8CDR_11 25S ribosomal RNA (chains AA)
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 12 (Aa), FASTA

>8CDR_12 Elongation factor 2 (chains Aa)
MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTR
KDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALR
VTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFAR
TVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKM
MDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLL
EKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGP
ADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVP
GKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKV
MKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEI
CLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLA
IENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIK
DSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLA
DPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGF
TGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYD
KL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	267
SPD	Spermidine	C7 H19 N3	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
SO1	[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-deox…	C27 H42 O8	1

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

Primary citation

mRNA reading frame maintenance during eukaryotic ribosome translocation. Milicevic, N., Jenner, L., Myasnikov, A. et al. Nature (2024) 625:393-400. DOI 10.1038/s41586-023-06780-4 · PubMed

Other PDB entries of the same protein (UniProt P0CX31 (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
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
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,…
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
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…

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