6OLE: 40S ribosomal protein SA

Name: PDB 6OLE: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs
Published: 2019-06-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs. Determined by electron microscopy at 3.1 Å resolution. Released 19 Jun 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 83
Atoms: 214,951
Mol. weight: 3176.91 kDa
Ligands: MG, ZN, MVM
Released: 19 Jun 2019

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

Secondary structure: helices and β-sheets

6OLE contains 463 α-helices and 561 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 a: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	69
β-strand	23-29	7	69
β-strand	40-48	9	69
α-helix	49-52	4
α-helix	61-64	4
β-strand	69-76	8	69
α-helix	77-79	3
β-strand	80-86	7	69
α-helix	109-122	14

Chain A: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	28	1	64
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-50	11	64
β-strand	57-64	8	64
β-strand	71-77	7	64
α-helix	78	1
β-strand	79	1	65
β-strand	83	1	66
β-strand	87-91	5	64
β-strand	101-103	3	64
β-strand	112-114	3	64
β-strand	116	1	67
β-strand	126	1	67
β-strand	134-137	4	64
β-strand	145-149	5	64
β-strand	155-159	5	64
β-strand	163-166	4	64
β-strand	169	1	65
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	68
α-helix	229-230	2
β-strand	237-238	2	68

Chain b: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	42-45	4
β-strand	72-74	3	76
α-helix	75-78	4
α-helix	84-90	7
β-strand	97-98	2	143
α-helix	99	1
β-strand	100-102	3	77
β-strand	110-112	3	76
β-strand	123-126	4	77
β-strand	128-129	2	76
α-helix	131-137	7
β-strand	143-146	4	77

Chain B: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	27-28	2
α-helix	32-34	3
α-helix	40-41	2
β-strand	45-55	11	71
β-strand	56-60	5	72
β-strand	70-72	3	72
β-strand	75-81	7	71
α-helix	82-83	2
β-strand	84-96	13	73
β-strand	98-106	9	73
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-146	7
α-helix	148-156	9
β-strand	159-165	7	73
α-helix	168-170	3
β-strand	180-184	5	73
α-helix	190-194	5
β-strand	203-205	3	73
β-strand	217-222	6	71
α-helix	223-225	3
β-strand	227-229	3	74
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-272	3	74
β-strand	276-282	7	71
β-strand	284-288	5	71
β-strand	320	1	75
β-strand	324	1	75
β-strand	329-334	6	71
β-strand	343-349	7	71
β-strand	365-368	4	72
α-helix	382-389	8

Chain c: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	37-50	14
α-helix	56-63	8
α-helix	95-99	5
α-helix	110-111	2
α-helix	112-116	5

Chain C: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	80
β-strand	17-23	7	80
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-44	11
α-helix	50-52	3
β-strand	64-66	3	81
β-strand	77-79	3	81
β-strand	90	1	81
α-helix	100-101	2
α-helix	117-129	13
α-helix	134-138	5
β-strand	152-154	3	80
α-helix	156-160	5
α-helix	164-173	10
α-helix	177-185	9
β-strand	189	1	82
α-helix	193-195	3
β-strand	201	1	82
β-strand	208-211	4	80
α-helix	217-220	4
β-strand	228-231	4	80
α-helix	237-240	4
α-helix	242-244	3
β-strand	250-253	4	80
α-helix	254-259	6
α-helix	260-262	3
α-helix	289-292	4
α-helix	298-301	4
α-helix	311-314	4
α-helix	316-317	2
α-helix	325-328	4
α-helix	331-364	34

Chain d: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
β-strand	26-29	4	85
α-helix	31-39	9
β-strand	45-49	5	85
α-helix	54-67	14
β-strand	70-74	5	85
α-helix	78-85	8
β-strand	93-98	6	85

Chain e: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	87
α-helix	29-32	4
α-helix	41-47	7
α-helix	50-56	7
β-strand	62-64	3	87
α-helix	66-72	7
β-strand	74	1	88
β-strand	76	1	88
β-strand	83-92	10	87
β-strand	102-108	7	87
β-strand	121-122	2	87

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
18S ribosomal RNA	S2	RNA	1714	Homo sapiens
40S ribosomal protein SA	SA	protein	221	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	214	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S3	SD	protein	226	Homo sapiens	P23396 (AlphaFold model)
40S ribosomal protein S4, X isoform	SE	protein	259	Homo sapiens	P62701 (AlphaFold model)
40S ribosomal protein S5	SF	protein	189	Homo sapiens	P46782
40S ribosomal protein S7	SH	protein	189	Homo sapiens	P62081
40S ribosomal protein S8	SI	protein	204	Homo sapiens	P62241
40S ribosomal protein S10	SK	protein	98	Homo sapiens	P46783
40S ribosomal protein S11	SL	protein	153	Homo sapiens	P62280
40S ribosomal protein S15	SP	protein	127	Homo sapiens	P62841
40S ribosomal protein S16	SQ	protein	146	Homo sapiens	P62249

71 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>6OLE_1 18S ribosomal RNA (chains S2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUA
ACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAU
CAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGG
UUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGC
GCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUU
UCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUCCGCGAGGAUCCAUUGGAGG
GCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCU
GCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGUCCCCGCCCUCUCGGCCGGGG
CCCGAAGCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUA
CCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAG
GCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUU
GGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAG
AACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUG
CCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAA
AGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAA
GGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAACCUCACCCG
GCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGU
GCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAC
UCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAG
GGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAU
GUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCA
GGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCC
AUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCC
UUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGG
CCCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAA
GGUUUCNGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (SA), FASTA

>6OLE_2 40S ribosomal protein SA (chains SA)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT

Sequence of entity 3 (SB), FASTA

>6OLE_3 40S ribosomal protein S3a (chains SB)
VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA
FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKA
CQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGE

Sequence of entity 4 (SD), FASTA

>6OLE_4 40S ribosomal protein S3 (chains SD)
AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE
KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYG
VLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGV
LGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 5 (SE), FASTA

>6OLE_5 40S ribosomal protein S4, X isoform (chains SE)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAKQ

Sequence of entity 6 (SF), FASTA

>6OLE_6 40S ribosomal protein S5 (chains SF)
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNS
MMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVR
RQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDE
LERVAKSNR

Sequence of entity 7 (SH), FASTA

>6OLE_7 40S ribosomal protein S7 (chains SH)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQ

Sequence of entity 8 (SI), FASTA

>6OLE_8 40S ribosomal protein S8 (chains SI)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKAR

Sequence of entity 9 (SK), FASTA

>6OLE_9 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR

Sequence of entity 10 (SL), FASTA

>6OLE_10 40S ribosomal protein S11 (chains SL)
ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCP
FTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQ
IGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQ

Sequence of entity 11 (SP), FASTA

>6OLE_11 40S ribosomal protein S15 (chains SP)
RTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPP
MEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHG
RPGIGAT

Sequence of entity 12 (SQ), FASTA

>6OLE_12 40S ribosomal protein S16 (chains SQ)
MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGK
ERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLL
VADPRRCESKKFGGPGARARYQKSYR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	31
ZN	Zinc ion	Zn	6
MVM	N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]py…	C22 H20 Cl N7 O	1

Primary citation

Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule. Li, W., Ward, F.R., McClure, K.F. et al. Nat Struct Mol Biol (2019) 26:501-509. DOI 10.1038/s41594-019-0236-8 · PubMed

Other PDB entries of the same protein (UniProt P08865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
3BCH 2.15 Å, Crystal Structure of the Human Laminin Receptor Precursor
7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

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