4V91: Kluyveromyces lactis 80S ribosome

Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES. Determined by electron microscopy at 3.7 Å resolution. Released 9 Jul 2014.

Method
Electron microscopy
Resolution
3.7 Å
Organism
KLUYVEROMYCES LACTIS
Chains
45
Atoms
125,665
Mol. weight
1977.86 kDa
Released
9 Jul 2014

Explore 4V91 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V91 contains 188 α-helices and 262 β-strands across 42 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: 3 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix7-104
β-strand7418
α-helix87-904
β-strand10219
α-helix104-1074
β-strand112110
β-strand11318
β-strand12519
β-strand130110
Chain A: 6 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix10-123
β-strand28111
β-strand42-44312
β-strand62-63212
β-strand72-73212
β-strand75111
α-helix861
β-strand87-89312
β-strand103113
α-helix104-1063
β-strand112-114314
β-strand116115
β-strand126115
β-strand134-136314
β-strand148-149214
β-strand163113
β-strand165-166214
α-helix174-1763
α-helix188-1903
β-strand224-225216
β-strand237-238216
Chain b: 2 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand22197
α-helix37-404
α-helix44-496
Chain B: 11 helices, 21 β-strands
ElementResiduesLengthSheet
α-helix27-282
α-helix32-343
β-strand45-53917
β-strand56-59418
β-strand71-74418
β-strand77-80417
α-helix82-832
β-strand84119
β-strand88-93620
β-strand100-106720
α-helix113-1175
α-helix148-1514
β-strand160-161220
β-strand164119
α-helix166-1683
β-strand180-181220
α-helix188-1958
β-strand203119
β-strand214-215221
β-strand219122
α-helix220-2234
β-strand225-226223
α-helix229-2335
α-helix235-2395
β-strand269-270223
β-strand275122
β-strand280-281221
β-strand285-286217
β-strand321-322217
β-strand334-339617
β-strand356-359418
α-helix373-3786
Chain c: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix11-2010
β-strand44124
α-helix50-6213
β-strand69124
Chain C: 11 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand6-7225
β-strand8-9226
β-strand15-16226
β-strand19-20225
α-helix24-274
α-helix35-439
β-strand76127
β-strand88127
α-helix115-1184
α-helix121-1244
β-strand150128
α-helix175-1839
β-strand186-187229
β-strand199-200229
β-strand206-209428
β-strand228-229228
β-strand248-250328
α-helix258-2625
α-helix276-2794
α-helix321-3244
α-helix330-3367
α-helix350-3523
α-helix355-3595
Chain d: 2 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand10130
β-strand13-15331
α-helix34-4411
β-strand49-51332
α-helix60-623
β-strand70-72331
β-strand74-75232
β-strand79133
β-strand89133
β-strand91-94432
β-strand108130
Chain D: 12 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix10-145
α-helix41-433
β-strand50-51234
β-strand64-65234
β-strand74134
α-helix83-864
α-helix98-1047
α-helix163-1686
β-strand183135
β-strand190135
α-helix195-1995
α-helix216-2216
α-helix224-2274
α-helix233-2353
α-helix238-2436
α-helix269-2713
α-helix280-2834

34 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
25S rRNA1RNA3397KLUYVEROMYCES LACTIS
5S rRNA3RNA121KLUYVEROMYCES LACTIS
5.8S rRNA4RNA158KLUYVEROMYCES LACTIS
UL2Aprotein254KLUYVEROMYCES LACTISP0CX45 (AlphaFold model)
UL3Bprotein387KLUYVEROMYCES LACTISP14126 (AlphaFold model)
UL4Cprotein362KLUYVEROMYCES LACTISP10664 (AlphaFold model)
UL18Dprotein297KLUYVEROMYCES LACTISP26321 (AlphaFold model)
EL6Eprotein176KLUYVEROMYCES LACTISQ02326
UL30Fprotein244KLUYVEROMYCES LACTISP05737
EL8Gprotein256KLUYVEROMYCES LACTISP17076
UL6Hprotein191KLUYVEROMYCES LACTISP05738
UL16Iprotein221KLUYVEROMYCES LACTISP41805

33 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>4V91_1 25S RRNA (chains 1)
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
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAAGGGAUGCGUAGGAU
AGGUGGGAGCGCAAGCGCCGGUGAAAUACCACCCUUCCCAUAGUUUCUUUACCUUAUUCA
AUGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUG
AUCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACG
AUAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGG
GUAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAU
CGAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUA
ACUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGC
UCUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGG
AACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUU
ACCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUG
CGGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCU
CUAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAU
ACGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGG
CGGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCA
UUUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUA
CGAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 2 (3), FASTA
>4V91_2 5S RRNA (chains 3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U
Sequence of entity 3 (4), FASTA
>4V91_3 5.8S RRNA (chains 4)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 4 (A), FASTA
>4V91_4 UL2 (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD
Sequence of entity 5 (B), FASTA
>4V91_5 UL3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 6 (C), FASTA
>4V91_6 UL4 (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 7 (D), FASTA
>4V91_7 UL18 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ
Sequence of entity 8 (E), FASTA
>4V91_8 EL6 (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 9 (F), FASTA
>4V91_9 UL30 (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 10 (G), FASTA
>4V91_10 EL8 (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 11 (H), FASTA
>4V91_11 UL6 (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL
Sequence of entity 12 (I), FASTA
>4V91_12 UL16 (chains I)
MARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQL
SSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWG
KPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPE
YLKKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFAAQA

Primary citation

Initiation of Translation by Cricket Paralysis Virus Ires Requires its Translocation in the Ribosome. Fernandez, I.S., Bai, X., Murshudov, G. et al. Cell (2014) 157:823. DOI 10.1016/J.CELL.2014.04.015 · PubMed

Other PDB entries of the same protein (UniProt P0CX45 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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