5IT7: Kluyveromyces lactis 80S ribosome

Name: PDB 5IT7: Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Published: 2016-05-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2. Determined by electron microscopy at 3.6 Å resolution. Released 18 May 2016.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Kluyveromyces lactis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Cricket paralysis virus
Chains: 83
Atoms: 215,768
Mol. weight: 3190.11 kDa
Ligands: 6EM, GCP, ZN, MG
Released: 18 May 2016

Explore 5IT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IT7 contains 494 α-helices and 653 β-strands across 78 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 1: 33 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-18	3
β-strand	19-21	3	52
β-strand	24-26	3	53
α-helix	34-41	8
α-helix	63-66	4
β-strand	74-75	2	54
α-helix	83-87	5
β-strand	99-101	3	52
β-strand	102-103	2	54
α-helix	110-112	3
α-helix	113-121	9
β-strand	126-130	5	53
β-strand	134	1	53
α-helix	137-144	8
β-strand	156-158	3	53
α-helix	171-191	21
β-strand	211-213	3	53
β-strand	218-220	3	53
α-helix	222-231	10
β-strand	249	1	55
β-strand	257	1	55
β-strand	262	1	56
β-strand	268	1	56
α-helix	273-277	5
α-helix	278-282	5
α-helix	283-290	8
α-helix	295-303	9
α-helix	309-312	4
α-helix	317-327	11
β-strand	329	1	53
α-helix	330-340	11
α-helix	345-356	12
β-strand	357	1	57
α-helix	364-371	8
β-strand	384	1	58
β-strand	387	1	59
β-strand	394	1	59
β-strand	396-400	5	58
β-strand	405	1	60
β-strand	409-411	3	61
β-strand	412-414	3	62
β-strand	426	1	62
β-strand	429-431	3	61
β-strand	433	1	63
β-strand	436	1	58
β-strand	438	1	64
β-strand	441	1	64
β-strand	448	1	60
β-strand	452-456	5	58
β-strand	457	1	63
β-strand	468-470	3	62
α-helix	475-477	3
β-strand	478	1	57
α-helix	479	1
β-strand	489-495	7	65
α-helix	501-512	12
β-strand	522	1	66
β-strand	528	1	66
β-strand	529-532	4	65
α-helix	536-544	9
α-helix	545-549	5
β-strand	554-557	4	65
α-helix	592-594	3
α-helix	595-603	9
α-helix	612-622	11
α-helix	627-631	5
β-strand	633-637	5	67
β-strand	644-647	4	67
α-helix	656-671	16
α-helix	709-720	12
β-strand	725-726	2	68
β-strand	729-732	4	69
α-helix	742-749	8
β-strand	753-754	2	69
β-strand	759	1	70
β-strand	766	1	70
β-strand	769-772	4	69
α-helix	780-788	9
β-strand	796-798	3	69
β-strand	802-803	2	68
α-helix	814-826	13

Chain a: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	195
β-strand	29-31	3	195
β-strand	39-43	5	196
α-helix	51-56	6
β-strand	57	1	108
β-strand	66-70	5	196
α-helix	75-79	5
α-helix	91-93	3
α-helix	97	1

Chain A: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	37	1	193
β-strand	48	1	193
α-helix	50-66	17
β-strand	74-77	4	194
α-helix	80-82	3
α-helix	83-92	10
β-strand	98-99	2	194
β-strand	121-123	3	194
α-helix	130-136	7
α-helix	137-139	3
β-strand	143-145	3	194
β-strand	159	1	194
α-helix	169-183	15
α-helix	199-201	3

Chain aa: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	29	1	24
β-strand	31	1	24
α-helix	42-46	5
β-strand	73-74	2	25
α-helix	77-81	5
β-strand	102-103	2	26
β-strand	111-113	3	25
β-strand	125-127	3	26
β-strand	129-130	2	25
α-helix	132-141	10
β-strand	145-147	3	26

Chain AA: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	30-32	3
α-helix	34-37	4
β-strand	41-42	2	30
β-strand	44-49	6	31
β-strand	58-62	5	31
β-strand	73-77	5	31
β-strand	79	1	32
β-strand	80	1	33
β-strand	82	1	33
β-strand	83	1	34
β-strand	89-90	2	30
β-strand	101-103	3	30
α-helix	104-106	3
β-strand	112-114	3	30
β-strand	116	1	35
β-strand	126	1	35
β-strand	134-136	3	30
β-strand	140	1	30
β-strand	145-149	5	30
β-strand	155-159	5	30
β-strand	163-166	4	30
β-strand	169	1	32
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	36
β-strand	237-238	2	36

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	205
β-strand	43-47	5	205
β-strand	54	1	206
β-strand	64-65	2	206
α-helix	71	1
β-strand	72-73	2	206
β-strand	78-80	3	205

Chain B: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	199
β-strand	31	1	200
β-strand	32-33	2	201
β-strand	45	1	200
β-strand	48	1	199
α-helix	57-61	5
β-strand	65	1	202
β-strand	68-69	2	203
α-helix	70-73	4
β-strand	83-85	3	203
β-strand	87	1	202
β-strand	91	1	201
β-strand	96-97	2	201
β-strand	102-104	3	203
α-helix	107-113	7
β-strand	125-128	4	203
β-strand	134-137	4	203
β-strand	142	1	204
α-helix	143-144	2
α-helix	155-157	3
α-helix	158-172	15
α-helix	182-188	7
α-helix	193-201	9
β-strand	208	1	204
β-strand	215-217	3	203
α-helix	225-231	7

Chain bb: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-19	8
β-strand	22	1	192
α-helix	37-57	21

70 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
25S ribosomal RNA	5	NA-hybrid	3270	Kluyveromyces lactis
5S ribosomal RNA	7	RNA	121	Kluyveromyces lactis
5.8S ribosomal RNA	8	RNA	157	Kluyveromyces lactis
KLLA0D16027p	AA	protein	249	Kluyveromyces lactis	Q6CQM3 (AlphaFold model)
60S ribosomal protein L3	BB	protein	384	Kluyveromyces lactis	Q6CJR7 (AlphaFold model)
KLLA0B07139p	CC	protein	360	Kluyveromyces lactis	Q6CW41 (AlphaFold model)
KLLA0D06941p	DD	protein	295	Kluyveromyces lactis	Q6CRR9 (AlphaFold model)
KLLA0B04686p	EE	protein	170	Kluyveromyces lactis	Q6CWE7
KLLA0D03410p	FF	protein	222	Kluyveromyces lactis	Q6CS71
KLLA0E00573p	GG	protein	233	Kluyveromyces lactis	B4UN96
KLLA0F04499p	HH	protein	191	Kluyveromyces lactis	Q6CLA6
KLLA0D05643p	II	protein	216	Kluyveromyces lactis	Q6CRX7

71 more molecules are not listed.

Sequence of entity 1 (5), FASTA

>5IT7_1 25S ribosomal RNA (chains 5)
UUGACCUCAAAUCAGGUAGGAAUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGAAA
AGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUGAA
AUCUGGCGUCUUCGACGUCCGAGUUGUAAUUUGAAGAAGGCAACUUUGUAGCUGGUCCUU
GUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAUCCC
AGUUAUUUGUAAAGUGCUUUCGACGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGGGU
GGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUGAU
GGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGGGA
AGGGCAUUUGAUCAGACAUGGGCCAGCAUCAGUUUUAGCGGUUGGAUAAAUCCUCGGGAA
UGUGGCUCUGCUUCGGUAGAGUGUUAUAGCCCGUGGGAAUACAGCCAGCUGGGACUGAGG
AUUGCGACUUUUGUCAAGGAUGCUGGCGUAAUGGUUAAAUGCCGCCCGUCUUGAAACACG
GACCAAGGAGUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCGUACGCGUAAUGAAA
GUGAACGUAGGUGAGGGCCCGCAAGGGUGCAUCAUCGACCGAUCCUGAUGUCUUCGGAUG
GAUUUGAGUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGG
UGAAGCCAGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUC
GAAUUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAG
UUUCCCUCAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGG
UACCGGGGUUGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGU
UGCUUAAUUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCA
GAACUGGCGAUGCGGGAUGAACCGAACGUGGAGUUAAGGUGCCGGAAUACACGCUCAUCA
GACACCACAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAU
CCGCUAAGGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCG
CUCAAGCGUGUUACCUAUACUCCACCGUCAGGGUUAAUAUGAUGCCCUGACGAGUAGGCA
GGCGUGGAGGUCAGUGACGAAGCCUAGGCUGUAAAGCUGGGUAGAACGGCCUCUAGUGCA
GAUCUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGG
UUCCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGU
UUCAAAGGCCUAAUUUUCUAGGCCACCAUCGAAAGGGAAUCCGGUUAAUAUUCCGGAACC
UGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGG
AGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAGGGG
GUCUUAUGGCUGGAAGAGCCCAGCCCUUGUGCUGGGUCCGGUGCGCCCGCGACGGCCCUU
GAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCU
CCAAGGUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGA
UCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGAUCGGGCGUGAGGGCCUUGGUCAGACG
CGGCGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGAUGCUGCAAUUAACGAUCAACUUAG
AACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUGGUCAG
AAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAU
UCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCC
UCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUAUCUA
CUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGAC
CCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGCAUAAGUG
GGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAAUUAAG
CGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAAGUCCUAUACGGGCUGAUCCGGG
UUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGAUAACGC
AGAUGUCCUAAGGGGGACUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGGUAAAAG
UCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUCGAUCCU
UUAGGUCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAACUGGCU
UGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCUCUUCCU
AUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGA
GCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUAUCGCAA
UAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUGU
CUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUCUAAGUC
AGAAUCCAUGCUAGAACGCGAUGAUUUCUUUGCCUUGCACAAUAUAGAAGGAUAAGAAUA
AGGCGUCUUUUUGGCGUCGCUGAACCAUAGCAGGCUGGCAACGGUGCUCUUAGCGGAAAG
GCUUUGGGUGCUUGCCGGCGAAUUGCAAUGUCAUUUUGCGCAAGGAUAAAUCAUUUGUAU
ACGACUUAAAUGUACAACAGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUACGAUCUG
CUGAGAUUAAGCCUUCGUUGUCUGAUUUGU

Sequence of entity 2 (7), FASTA

>5IT7_2 5S ribosomal RNA (chains 7)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 3 (8), FASTA

>5IT7_3 5.8S ribosomal RNA (chains 8)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAUUGCGAU
AUGUAUUGUGAAUUGCAGAUUUUCGUGAAUCAUCAAAUCUUUGAACGCACAUUGCGCCCU
CUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUU

Sequence of entity 4 (AA), FASTA

>5IT7_4 KLLA0D16027p (chains AA)
GRVIRNQRKGAGSIFTSHTRLRQGAAKLRNLDYAERHGYIRGVVKQIVHDAGRGAPLAKV
VFRDPYKYKLREETFIANEGLHTGQFIYAGKKASLNVGNVLPLGSVPEGTIISNVEERPG
DRGALARASGNYVIVIGHNPEDNKTRVRLPSGAKKIISSDARGVIGVVAGGGRIDKPLLK
AGRAFHKYRVKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAAR
RTGLLRGSQ

Sequence of entity 5 (BB), FASTA

>5IT7_5 60S ribosomal protein L3 (chains BB)
SHRKYEAPRHGHLGFLPRKRAASVRGRVKSFPKDDQTKPVALTSFLGYKAGMSTIVRDLD
RPGSKFHKREVVEAVTVVDTPPIVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKN
WYKSKKKAFTKYSAKYAENGAQVDRELARIKKYASVVRVLVHTQVRKTPLSQKKAHLAEI
QLNGGSVSDKVDWAKEHFEKTVAVDSVFEQNEMIDVVAVTKGHGFEGVTHRWGTKKLPRK
THRGLRKVACIGAWHPAHVMWSVARAGQRGYHHRTSINHKVYRVGKGDDEANAATEFDRT
KKTITPMGGFVHYGAINNDFVILKGSIPGTRKRVVTLRKSLYTNTSRKALEEVTLKWIDT
ASKFGKGRFQTPAEKHAFLGTLKK

Sequence of entity 6 (CC), FASTA

>5IT7_6 KLLA0B07139p (chains CC)
RPQVAVLSLNGETTSTDLPLPAVFRAPIRPDIVHSVFTSVNKNKRQAYAVSEKAGHQTSA
ESWGTGRAVARIPRVGGGGTHRSGQAAFGNMCRGGRMFAPTKTWRKWNVKVNQNEKRYAT
ASAIAASAVPSLVLARGHRVEKVPSIPLVVSDDLQSIQKTKEAVAALKAVGAHSDVIKVV
KSKKLRAGKGKYRNRRFTQRRGPLVVYSEDNGVVKAFRNVPGVETANVASLGLLQLAPGA
HLGRFVIWTQSAFSKLDQIWGSETVASVKAGYALPSNIISTSDVTRIINSTEIQSVLRAA
GQATQKRTHVQKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKVDQANKIKPSATALETLKH

Sequence of entity 7 (DD), FASTA

>5IT7_7 KLLA0D06941p (chains DD)
FIKDIKTSAYHSRYQTPFRRRREGKTDYYARKRLVAQHKAKYNTPKYRLVVRFTNKDIIT
QIVSSTITGDIVLAAAYSHELPRYGITHGLTNWSAAYATGLLLARRTLQKLGLDETYPGV
EEVEGEYELTEAVEDGPRPFKVYLDVGLQRTTTGARIFGALKGASDGGLYVPHSENRFPG
WDFEAEELDADLLRTYIFGGHVSQYMEELADDDEERYRELFKGYLADDIDADAVEDIYAD
AHAAIREDPAFKPTEKKFTKEQYAAESKKYRQVKLTREERKARVAAKISALAPQE

Sequence of entity 8 (EE), FASTA

>5IT7_8 KLLA0B04686p (chains EE)
KWYPAEEVPAPKQTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLVSG
PFKVNGVPLRRVNARYVIATSTRVSLEGVNTEKFNVAYFSREKLSRKQRAEANFFNEDQP
KKEIKAERIEDQKNIDKALLAEIKKTPLLKQYLAATFSLKNGDRPHLLKF

Sequence of entity 9 (FF), FASTA

>5IT7_9 KLLA0D03410p (chains FF)
QKTAEQVAAERVARKAEKRAAILERNAAYQKEYETAERAVIDAKREAKANSSYYVSAEAK
LVFVVRIKGINKIPPKPRKVLQLLRLNQINSGTFVKVTKATSELLKLIEPYVAYGYPSYS
TVRQLVYKRGYGKINKQRIPLSDNSIVEANLGNYGILSVDDLIHEIVTVGPHFKQANNFL
WPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLVKSMN

Sequence of entity 10 (GG), FASTA

>5IT7_10 KLLA0E00573p (chains GG)
NPLTKSSPRNFGIGQAIQPKRNLSRYVKWPEYVRLQRQKKILSIRLKVPPSIAQFQNTLD
RNTAAETFKLLKKYSPETAAEKKERLTKEAAAIAEGKTKQEASPKPYVVKYGLNHVVSLI
ENKKAKLVLIANDVDPIELVIFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEV
REEDEAALAKLVSTINANYLEKYEDSKKHWGGGIMGQKAQKKIEKRAKAAESA

Sequence of entity 11 (HH), FASTA

>5IT7_11 KLLA0F04499p (chains HH)
MKYIQTDQVLDVPEGVTVQIRSRIIKVTGPRGVLTKNLKHIDVTFTKVSNRQIKITVHNG
DRKHVAALRTVKSLISNLITGVTKGYKYKLRYVYAHFPINVNVIEKDGAKFIEIRNFLGD
KKVREVPVREGVSVDFSTNQKDEIVLSGNSVENVSQNAADIQQICRVRNKDIRKFLDGIY
VSEKGLIEEEE

Sequence of entity 12 (II), FASTA

>5IT7_12 KLLA0D05643p (chains II)
RRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSS
EALEAARITANKYITKMTGRDSFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKP
HGLAARVAIGQVIFSVRTKDNNKDTVIEGLRRARYKFPGQQKIIISKKWGFTSLNREEYV
KKRDAGEIKDDGAFVKFLSKKGSLEENIREFPEYFA

Ligands and cofactors

ID	Name	Formula	Copies
6EM	(2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium	C7 H17 N2 O	1
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	80

Primary citation

Structural characterization of ribosome recruitment and translocation by type IV IRES. Murray, J., Savva, C.G., Shin, B.S. et al. Elife (2016) 5. DOI 10.7554/eLife.13567 · PubMed

Other PDB entries of the same protein (UniProt Q6CQM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B

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