4V7E: 40S ribosomal protein S24E

Name: PDB 4V7E: Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome. Determined by electron microscopy at 5.5 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 5.5 Å
Organism: Triticum aestivum
Chains: 88
Atoms: 212,263
Mol. weight: 3326.88 kDa
Released: 9 Jul 2014

Explore 4V7E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V7E contains 473 α-helices and 505 β-strands across 82 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 Ba: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	34
β-strand	29-31	3	34
α-helix	32-35	4
β-strand	39-42	4	35
α-helix	49-55	7
β-strand	57	1	110
β-strand	67-70	4	35
α-helix	76-79	4
α-helix	89-93	5

Chain BA: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	16-25	10
β-strand	29	1	6
α-helix	45	1
β-strand	46	1	7
β-strand	50	1	7
β-strand	52	1	6
α-helix	55-69	15
α-helix	75-77	3
β-strand	79-82	4	8
α-helix	85-97	13
β-strand	101-104	4	8
β-strand	126-128	3	8
α-helix	135-143	9
β-strand	149-152	4	8
β-strand	164-166	3	8
α-helix	174-188	15

Chain Bb: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
β-strand	34-38	5	171
β-strand	46-49	4	171
β-strand	57	1	172
β-strand	65	1	172
β-strand	66-67	2	173
β-strand	74-75	2	173
β-strand	80-82	3	171

Chain BB: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	19
β-strand	42-46	5	19
α-helix	57-60	4
β-strand	65-69	5	20
α-helix	71-74	4
β-strand	83-87	5	20
β-strand	91-92	2	19
β-strand	95-96	2	19
β-strand	99-100	2	20
β-strand	102-103	2	21
α-helix	107-113	7
β-strand	121-128	8	22
β-strand	134-141	8	22
α-helix	143-145	3
α-helix	159-175	17
α-helix	180-188	9
α-helix	192-201	10
β-strand	215-216	2	21
α-helix	225-228	4
α-helix	229-231	3

Chain Bc: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	153
β-strand	26-29	4	153
β-strand	37-40	4	153

Chain BC: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-46	7
α-helix	53-58	6
α-helix	67-72	6
β-strand	77	1	44
β-strand	80-85	6	45
β-strand	91	1	46
β-strand	93	1	46
β-strand	98-103	6	45
β-strand	105	1	44
β-strand	110-111	2	47
β-strand	113-118	6	45
α-helix	121-134	14
β-strand	137-138	2	47
β-strand	158-162	5	48
β-strand	165-170	6	48
β-strand	178-179	2	48
α-helix	182-191	10
β-strand	196-201	6	48
α-helix	207-219	13
α-helix	220-223	4
α-helix	227-230	4
α-helix	239-242	4

Chain Bd: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	40-45	6

Chain BD: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
β-strand	37-38	2	74
β-strand	41-42	2	75
β-strand	45-46	2	75
β-strand	49-51	3	74
α-helix	55-58	4
α-helix	65-76	12
β-strand	87-89	3	74
α-helix	100-106	7
α-helix	115-124	10
α-helix	126-129	4
β-strand	133-137	5	76
β-strand	138	1	77
α-helix	142-144	3
β-strand	150	1	77
β-strand	153-155	3	76
β-strand	168-170	3	76
β-strand	176	1	78
β-strand	181	1	78
β-strand	185-189	5	76

73 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	Ad	RNA	1810	Triticum aestivum
P-site tRNA	Ae	RNA	75	Triticum aestivum
5'-r(apapapapgpapcpupupcp*a)-3'	Af	RNA	11	Triticum aestivum
40S ribosomal protein S24E	BY	protein	138	Triticum aestivum
40S ribosomal protein S8E	BI	protein	220	Triticum aestivum
40S ribosomal protein S10E	BK	protein	183	Triticum aestivum
40S ribosomal protein S12E	BM	protein	171	Triticum aestivum
40S ribosomal protein S31e	Bf	protein	155	Triticum aestivum
40S ribosomal protein S12	BX	protein	142	Triticum aestivum
RACK1	Bg	protein	380	Triticum aestivum	Q8LNY6 (AlphaFold model)
40S ribosomal protein S3	BD	protein	208	Triticum aestivum	Q8L804 (AlphaFold model)
40S ribosomal protein S4E	BE	protein	265	Triticum aestivum

74 more molecules are not listed.

Sequence of entity 1 (Ad), FASTA

>4V7E_1 18S ribosomal RNA (chains Ad)
UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGC
AAGUAUGAACCAAUUUGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUG
UUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAA
CCCCGACUUCUGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCUCGCU
GAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAU
UCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGG
GUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCA
AGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAU
AACAAUACCGGGCGCAUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAC
GAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGC
GUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGUCGGCCGG
UCCGCCUCACGGCGAGCACCGACCUACUCGACCCUUCGGCCGGCAUCGCGCUCCUAGCCU
UAAUUGGCCGGGUCGUGUUUCCGGCAUCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCA
AGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGU
UGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAG
UCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGA
UGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGU
CUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGC
ACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACU
UAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGCUUAAUUUGACUCAACA
CGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGA
UUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUC
CGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUA
GCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGU
CAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUAUAUA
GCCUUGGCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUU
GCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAC
UACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAA
GUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUG
AACCUUAUCAUUUAGAGGAAGCAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGA
AGGAUCAUUG

Sequence of entity 2 (Ae), FASTA

>4V7E_2 P-site tRNA (chains Ae)
UCCGUGAUAGUUUAAUGGUCAGAAUGGGCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUUC
CCCGUCGCGGAGCCA

Sequence of entity 3 (Af), FASTA

>4V7E_3 5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3' (chains Af)
AAAAGACUUCA

Sequence of entity 4 (BY), FASTA

>4V7E_4 40S ribosomal protein S24E (chains BY)
MADTKTAPAVTLRTRKFMTNRLLSRKQFVLEVLHPGRANVSKADLKEKLAKLYEVKDSNC
IFVFKFRTHFGGGKSTGFGLIYDNLDAAKKYEPKYRLIRNGLATKVEKSRKQMKERKNRA
KKIRGVKKTKAGDAGKKK

Sequence of entity 5 (BI), FASTA

>4V7E_5 40S ribosomal protein S8E (chains BI)
MGISRDSMHKRRATGGKQKAWRKKRKYELGRQPANTKLSSNKTVRRVRVRGGNVKWRALR
LDTGNYSWGSEAVTRKTRILDVVYNASNNELVRTQTLVKSAIVQVDAAPFKQWYLTHYGV
DIGRKKKAPAAKKDAEGQDAEATTEEAKKSNHVVRKLEKRQQGRTLDAHIEEQFGSGRLL
ACISSRPGQCGRADGYILEGKELEFYMKKLQRKKGKGASA

Sequence of entity 6 (BK), FASTA

>4V7E_6 40S ribosomal protein S10E (chains BK)
MIIPKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFS
WQYYYWYLTNDGIEHLRNYLNLPSEIVPATLKKSARPPGRPFGSGPPGDRPRGPPRFEGD
RPRFGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGRPGFGRGGGGGFGAGPTSS
SME

Sequence of entity 7 (BM), FASTA

>4V7E_7 40S ribosomal protein S12E (chains BM)
LTLLAKTLTPPPPPLFATRSFRRSRCSGLLSAEMAEETPVETPAAPVLGEPMDLMTALQL
VMKKSSAHDGLVKGLREAAKAIEKHAAQLCVLAEDCDQPDYVKLVKALCAEHNVHLVTVP
SAKTLGEWAGLCKIDSEGKARKVVGCSCVVVKDYGEESEGLNIVQDYVKSH

Sequence of entity 8 (Bf), FASTA

>4V7E_8 40S ribosomal protein S31e (chains Bf)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
IQKESTLHLVLRLRGGAKKRKKKTYTKPKKIKHKHKKVKLAVLQFYKVDDATGKVTRLRK
ECPNNDCGAGTFMANHFDRHYCGKCGLTYVYNQKA

Sequence of entity 9 (BX), FASTA

>4V7E_9 40S ribosomal protein S12 (chains BX)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS

Sequence of entity 10 (Bg), FASTA

>4V7E_10 RACK1 (chains Bg)
MASVAELKEKHAAATASVNSLRERLRQRRQTLLDTDVEKYSKAQGRTAVSFNPTDLVCCR
TLQGHSGKVYSLDWTPEKNWIVSASQDGRLIVWNALTSQKTHAIKLHCPWVMECAFAPNG
QSVACGGLDSACSIFNLSSQADRDGNMPVSRVLTGHKGYASSCQYVPDQETRLITGSGDQ
TCVLWDVTTGQRISIFGSEFPSGHTADVLSLSINSLNANMFISGSCDTTVRLWDLRITSR
AVRTYHGHEGDINSVKFFPDGQRFGTGSDDGTCRLFDMRTGHQLQVYNREPDRNDNELPI
VTSVAFSISGRLLFAGYSNGDCYVWDTLLAEMVLNLGTLQNSHEGRISCLGLSSDGSALC
TGSWDKNLKIWAFSGHRKIV

Sequence of entity 11 (BD), FASTA

>4V7E_11 40S ribosomal protein S3 (chains BD)
VSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTS
VVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGA
KGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKVKIMLD
WDPKGKLGPTTPLPDLVTIHPPKEENEL

Sequence of entity 12 (BE), FASTA

>4V7E_12 40S ribosomal protein S4E (chains BE)
MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYRE
VISILMQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAK
FKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNV
VMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPK
GKGIKLSIIEEQRKRDAAAQAAANA

Primary citation

Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Gogala, M., Becker, T., Beatrix, B. et al. Nature (2014) 506:107-110. DOI 10.1038/nature12950 · PubMed

Other PDB entries of the same protein (UniProt Q8LNY6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V3P 34.0 Å, The molecular structure of the left-handed supra-molecular helix of eukaryotic…

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