8JIV: PDB entry 8JIV

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes. Determined by electron microscopy at 2.84 Å resolution. Released 27 Mar 2024.

Method
Electron microscopy
Resolution
2.84 Å
Organism
Triticum aestivum
Chains
44
Atoms
116,711
Mol. weight
1984.47 kDa
Ligands
MG, ZN
Released
27 Mar 2024

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

Secondary structure: helices and β-sheets

8JIV contains 324 α-helices and 291 β-strands across 41 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 Ca: 9 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix3-53
α-helix9-113
α-helix42-487
α-helix65-684
β-strand72-7434
α-helix75-817
α-helix84-896
β-strand95-9955
α-helix100-1034
β-strand107-10934
α-helix113-1153
β-strand120-12345
β-strand125-12624
α-helix128-1369
β-strand140-14345
Chain CA: 11 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix6-94
α-helix10-123
β-strand2816
α-helix29-324
α-helix34-385
β-strand41-4996
β-strand58-6476
β-strand71-7776
α-helix781
β-strand7917
β-strand8318
β-strand87-9046
β-strand101-10336
α-helix104-1063
β-strand112-11436
β-strand11619
β-strand12619
β-strand134-14076
β-strand145-14956
β-strand155-15956
β-strand163-16646
β-strand16917
α-helix174-1763
α-helix182-1909
α-helix198-2003
α-helix201-2033
β-strand224-225210
α-helix229-2302
β-strand237-238210
Chain Cb: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix12-176
β-strand22182
α-helix23-253
α-helix40-489
Chain CB: 20 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix9-102
α-helix14-163
α-helix32-354
α-helix40-412
β-strand43111
β-strand45-591512
β-strand71-801012
α-helix82-832
β-strand84-931013
β-strand100-106713
α-helix112-1154
α-helix116-1183
α-helix133-1375
α-helix141-15616
β-strand159-165713
α-helix168-1703
α-helix172-1743
α-helix179-1802
β-strand181-185513
β-strand186111
α-helix191-1999
β-strand202113
β-strand205-206213
α-helix208-2103
β-strand217-223712
β-strand226-230514
α-helix232-2354
α-helix238-2425
β-strand271-274414
β-strand277-2891312
α-helix294-2963
α-helix3111
β-strand315115
β-strand319115
β-strand325-329512
β-strand339-344612
α-helix352-3554
β-strand360-363412
α-helix377-3848
Chain Cc: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix15-2410
β-strand26-29416
α-helix31-399
β-strand45-48416
α-helix54-6613
β-strand70-73416
α-helix80-834
β-strand93-98616
Chain CC: 26 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand8-10317
β-strand11-12218
β-strand25-27317
α-helix28-292
α-helix30-334
α-helix38-4912
α-helix50-523
α-helix53-553
β-strand69-70219
β-strand81-82219
β-strand94119
α-helix108-1103
α-helix121-13414
α-helix138-1436
β-strand157-158218
α-helix160-1645
α-helix168-17710
α-helix181-1888
β-strand192-193220
α-helix194-1952
α-helix197-1993
β-strand205-206220
β-strand212-215418
α-helix222-2265
β-strand233-236418
α-helix237-2393
α-helix242-2454
α-helix247-2493
β-strand255-258418
α-helix259-2646
α-helix284-2874
α-helix294-2985
α-helix301-3044
α-helix307-3104
α-helix317-3204
α-helix327-3326
α-helix339-3457
α-helix372-38514
Chain Cd: 5 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand18-25821
α-helix26-294
α-helix35-373
α-helix38-5417
β-strand58-61421
α-helix63-708
β-strand80-891021
β-strand99-105721
α-helix106-1083
β-strand119-120221
Chain CD: 17 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix11-166
α-helix19-213
α-helix22-254
α-helix31-388
α-helix42-443
β-strand51-56622
β-strand61-69922
β-strand72-80922
α-helix84-863
α-helix96-11318
α-helix133-1353
α-helix140-1423
β-strand143123
β-strand145-147322
α-helix158-16912
β-strand172123
β-strand183-184224
β-strand189-190224
α-helix192-1998
α-helix202-21211
α-helix216-2227
α-helix224-2285
α-helix236-24914
α-helix268-2725
α-helix273-28816

33 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 rRNAAaRNA3391Triticum aestivum
5S rRNAAbRNA119Triticum aestivum
5.8S rRNAAcRNA158Triticum aestivum
Ribosomal protein L2 C-terminal domain-containing proteinCAprotein261Triticum aestivumW5ECL2 (AlphaFold model)
Ribosomal protein L3CBprotein385Triticum aestivumQ7X744 (AlphaFold model)
60S ribosomal protein L4 C-terminal domain-containing proteinCCprotein405Triticum aestivum
Ribosomal protein L5 eukaryotic C-terminal domain-containing proteinCDprotein307Triticum aestivumA0A3B6DD91 (AlphaFold model)
60S ribosomal protein L6CEprotein232Triticum aestivumA0A3B6QGW3 (AlphaFold model)
60S ribosomal protein uL30CFprotein244Triticum aestivumA0A3B6DM38
60S ribosomal protein L7aCGprotein258Triticum aestivumA0A3B6RED0
Ribosomal protein L6 alpha-beta domain-containing proteinCHprotein189Triticum aestivumA0A9R1FDI5
Ribosomal protein L10e/L16 domain-containing proteinCIprotein217Triticum aestivumA0A3B6HUM3

32 more molecules are not listed.

Sequence of entity 1 (Aa), FASTA
>8JIV_1 25S rRNA (chains Aa)
GCGACCCCAGGUCAGGCGGGACUACCCGCUGAGUUUAAGCAUAUAAAUAAGCGGAGGAGA
AGAAACUUACAAGGAUUCCCCUAGUAACGGCGAGCGAACCGGGAGCAGCCCAGCUUGAGA
AUCGGGCGGCUGUGCCGUCCGAAUUGUAGUCUGGAGAGGCGUCCUCAGCGACGGACCGGG
CCCAAGUCCCCUGGAAAGGGGCGCCUGGGAGGGUGAGAGCCCCGUCCGGCCCGGACCCUG
UCGCCCCACGAGGCGCCGUCAACGAGUCGGGUUGUUUGGGAAUGCAGCCCAAAUCGGGCG
GUAGACUCCGUCCAAGGCUAAAUACAGGCGAGAGACCGAUAGCGAACAAGUACCGCGAGG
GAAAGAUGAAAAGGACUUUGAAAAGAGAGUCAAAGAGUGCUUGAAAUUGCCGGGAGGGAA
GCGGAUGGGGGCCGGCGAUGCGCCCCGGCCGUAUGCGGAACGGCUCUUGCUGGUCCGCCG
CUCGGCUCGGGGUGUGGACUGUUGUCGGCCGCGCCGGCGGCCAAAGCCCGGGGGCCCUAG
GUGCCCCCGGUGGCCGUCGUCGGCACGGCCGGUACCCGCGCGCCUAAAGGCGUGUCCCUC
GGGGCACUGCGCUGCAACGGCCUGCGGGCUCCCCAUCCGACCCGUCUUGAAACACGGACC
AAGGAGUCUGACAUGCGUGCGAGUCGACGGGUUCUGAAACCUGGGAUGCGCAAGGAAGCU
GACGAGCGGGAGGCCCUCACGGGCCGCACCGCUGGCCGACCCUGAUCUUCUGUGAAGGGU
UCGAGUUGGAGCACGCCUGUCGGGACCCGAAAGAUGGUGAACUAUGCCUGAGCGGGGCGA
AGCCAGAGGAAACUCUGGUGGAGGCUCGAAGCGAUACUGACGUGCAAAUCGUUCGUCUGA
CUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUU
CCCUCAGGAUAGCUGGAGCCCAUUACGAGUUCUAUCAGGUAAAGCCAAUGAUUAGAGGCA
UUGGGGACGCAACGUCCUCGACCUAUUCUCAAACUUUAAAUAGGUAGGAUGGCGCGGCUG
CUUCGGUGAGCCGUGCCAUGGAAUCGGGUGCUCCAAGUGGGCCAUUUUUGGUAAGCAGAA
CUGGCGAUGCGGGAUGAACCGGAAGCCGGGUUACGGUGCCCAACUGCGCGCUAACCUAGA
ACCCACAAAGGGUGUUGGUCGAUUAAGACAGCAGGACGGUGGUCAUGGAAGUCGAAAUCC
GCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCCGAAAAUGGAUGGCGCU
GAAGCGCGCGACCCACACCCGGCCAUCUGGGCGAGCGCCAUGCCCCGAUGAGUAGGAGGG
CGCGGCGGCCGCUGCAAAACCCGGGGCGCGAGCCCGGGCGGAGCGGCCGUCGGUGCAGAU
CUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGGCCGAAGAGGAGAAAGGUUC
CAUGUGAACGGCACUUGCACAUGGGUAAGCCGAUCCUAAGGGACGGGGUAACCCCGGCAG
AUAGCGCGAUCACGCGCAUCCCCCGAAAGGGAAUCGGGUUAAGAUUUCCCGAGCCGGGAU
GUGGCGGUUGACGGCGACGUUAGGAAGUCCGGAGACGCCGGCGGGGGCCUCGGGAAGAGU
UAUCUUUUCUGCUUAACGGCCUGCCAACCCUGGAAACGGUUCAGCCGGAGGUAGGGUCCA
GUGGCCGGAAGAGCACCGCACGUCGCGCGGUGUCCGGUGCGCCCCCGGCGGCCCAUGAAA
AUCCGGAGGACCGAGUACCGUUCACGCCCGGUCGUACUCAUAACCGCAUCAGGUCUCCAA
GGUGAACAGCCUCUGGCCAAUGGAACAAUGUAGGCAAGGGAAGUCGGCAAAACGGAUCCG
UAACUUCGGGAAAAGGAUUGGCUCUGAGGACUGGGCUCGGGGGUCCCGGCCCCGAACCCG
UCGGCUGUCGGCGGAUUGCUCGAGCUGCUCACGCGGCGAGAGCGGGUCGCCGCGUGCCGG
CCGGGGGACGGACCGGGAAUCGCCCCUUCGGGGGCUUUCCCCGAGCAUGAAACAGUCGAC
UCAGAACUGGUACGGACAAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUUGCGAUGG
UCCUCGCGGAUGCUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGA
AAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAU
GCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUGU
CUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAA
GACCCUGUUGAGCUUGACUCUAGUCCGACUUUGUGAAAUGACUUGAGAGGUGUAGGAUAA
GUGGGAGCCCUCACGGGCGCAAGUGAAAUACCACUACUUUUAACGUUAUUUUACUUAUUC
CGUGGGUCGGAAGCGGGGCAUGUCCCCUCCUUUUGGCUCCAAGGCCCGGUCUUACCGGGC
CGAUCCGGGCGGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAA
AGAUAACGCAGGUGUCCUAAGAUGAGCUCAACGAGAACAGAAAUCUCGUGUGGAACAAAA
GGGUAAAAGCUCGUUUGAUUCUGAUUUCCAGUACGAAUACGAACCGUGAAAGCGUGGCCU
AUCGAUCCUUUAGAUCUUCGGAGUUUGAAGCUAGAGGUGUCAGAAAAGUUACCACAGGGA
UAACUGGCUUGUGGCAGCCAAGCGUUCAUAGCGACGUUGCUUUUUGAUCCUUCGAUGUCG
GCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGUGUUGGAUUGUUCACCCACCAAUAG
GGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGACAG
UGUCGCGAUAGUAAUUCAACCUAGUACGAGAGGAACCGUUGAUUCACACAAUUGGUCAUC
GCGCUUGGUUGAAAAGCCAGUGGCGCGAAGCUACCGUGUGCCGGAUUAUGACUGAACGCC
UCUAAGUCAGAAUCCAAGCUAGCAUGCGACGCCUGCGCCCGCCGCCCGCCCCGACCCACG
UUAGGGGCGCUUGCGCCCCCAAGGGCCCGUGCCAUUGGCUAAGCCGGUCCGGCCGAAGUG
CCGCGGCCGGCCGCCUCGAAGCUCCCUUCCCAACGGGCGGUGGGCUGAAUCCUUUGCAGA
CGACUUAAAUACGCGACGGGGCAUUGUAAGUGGCAGAGUGGCCUUGCUGCCACGAUCCAC
UGAGAUCCAGCCCCAUGUCGCACGGAUUCGU
Sequence of entity 2 (Ab), FASTA
>8JIV_2 5S rRNA (chains Ab)
GGAUGCGAUCAUACCAGCACUAAGGCAUCGGAUCCCGUCAGAACUCCGAAGUUAAGCGUG
CUUGGGCGAGAGUAGUACAAGGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCAUUCC
Sequence of entity 3 (Ac), FASTA
>8JIV_3 5.8S rRNA (chains Ac)
CGACUCUCGGCAACGGAUAUCUCGGCUCUCGCAUCGAUGAAGAACGUAGCGAAAUGCGAU
ACCUGGUGUGAAUUGCAGAAUCCGUGAACCAUCGAGUCUUUGAACGCAAGUUGCGCCCGA
GGCCACUCGGCCGAGGGCACGCCUGCCUGGGCGUCACG
Sequence of entity 4 (CA), FASTA
>8JIV_4 Ribosomal protein L2 C-terminal domain-containing protein (chains CA)
MGRVIRAQRKGAGSVFKSHTHHRKGPARFRSLDFGERNGYLKGVVTDVIHDPGRGAPLAK
VTFRHPFRYKHQKELFVAAEGMYTGQFVYCGRRATLSVGNVLPLRSVPEGGVICNVEHHV
GDRGVFARASGDYAIVISHNPDNGTSRIKLPSGAKKIVPSSCRAMIGQVAGGGRTEKPML
KAGNAYHKYRVKRNSWPKVRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVGLIAA
RRTGRLRGQAAASAAKADKAT
Sequence of entity 5 (CB), FASTA
>8JIV_5 Ribosomal protein L3 (chains CB)
MSHRKFEHPRHGSLGFLPRKRCSRHRGKVKSFPKDDQQKPCHLTAFLGYKAGMTHIVREV
EKPGSKLHKKETCEAVTIIETPPLVIVGLVAYVKTPRGLRTLNSVWAQHLSEDVRRRFYK
NWCKSKKKAFTKYALKYDSDAGKKEIQLQLEKMKKYATIVRVIAHTQIRKMKGLKQKKAH
LMEIQVNGGTIADKVDYGYKFFEKEVPVEAVFQKDEMVDIIGVTKGKGYEGVVTRWGVTR
LPRKTHRGLRKVACIGAWHPARVSYTVARAGQNGYHHRTEMNKKIYKMGKSGQESHEACT
EFDRTEKDITPMGGFPHYGVVKGDYLMIKGCCVGPKKRVVTLRQSLLKQTSRLALEEIKL
KFIDTSSKFGHGRFQTTDEKQKFYG
Sequence of entity 6 (CC), FASTA
>8JIV_6 60S ribosomal protein L4 C-terminal domain-containing protein (chains CC)
MATQTRPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSR
RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVN
VHLRRVAVASALAATSVPSLVLARGHRIETVPELPLVISDSAESIEKTSQAIKILKQVGA
YADAEKAKDSVGIRPGKGKMRNRRYINRKGPLIVYGTEGSKIVKAFRNLPGVDVANVERL
NLLDLAPGGHLGRFVIWTESAFKKLEEVYGTFEAPSLKKKGFILPRPKMANADLGRIINS
DEVQSVVKPLNKEVKRREKRKNPLKNVAAVLKLNPYFGTARKMATLAEAARIKARKEKLD
SKRTKLSPEEAAKVKAAGKAWYKTMISDSDYAEFDNFSKWLGVTQ
Sequence of entity 7 (CD), FASTA
>8JIV_7 Ribosomal protein L5 eukaryotic C-terminal domain-containing protein (chains CD)
MFWMDFQVFVKNQKTRAYSKRFQVKFKRRRQGKTDYRARLRLTNQDKNKYNTPKYRFVVR
FTNKDVTAQIVYATIAGDIVMAAAYSHELPRYGLEVGLTNYAAAYCTGLLLARRVLKCRD
LDQEYEGNVEATGEDFSVEPADERRPFRALLDVGLIRTTTGNRVFGALKGALDGGLDIPH
SDKRFAGFKKDEKQLDAEIHRKYIYGGHVADYMKSLADEEPEKYQSHFSEYIKKGIEADN
MEALYKKVHAAIRADPTMAKSTKEPPKTHKRYNPKKLTYEQRKASLVERLNALNSSAGAD
VDEDDDE
Sequence of entity 8 (CE), FASTA
>8JIV_8 60S ribosomal protein L6 (chains CE)
SPDCRSASTEESPMAPTSKMALGIKRASRSHTYHRRGLWAIKAKHGGALPKAEKPAAVAE
PKFYPADDVKPRTVSTRKPHPTKLRSTITPGTVLILLAGRYMGKRVVFLKQLQSGLLLIT
GPFKINGVPIRRVNQAYVIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDK
EATKNLPDFKKDDQKVIDAELIKAIDAVPDLKNYLGARFSLRDGDKPHEMTF
Sequence of entity 9 (CF), FASTA
>8JIV_9 60S ribosomal protein uL30 (chains CF)
MASEAAKVAVPEKVILKRRREEVWAAEKKQKVAAEKIKAAENTKVIYARAEQYAGEYEAQ
DKELVQLKREARMKGGFYVSPEAKLLFVVRIRGINAMHPKTKKILQLLRLRQIFNGVFLK
VNKATINMLRRVEPYVAYGYPNLKSVRELIYKRGYGKLNKQRIPLANNKVIEEGLGKHNI
ICIEDLVHEILTVGPHFKEANNFLWPFKLKAPLGGLKKKRNHYVEGGDAGNRENYINQLV
RRMN
Sequence of entity 10 (CG), FASTA
>8JIV_10 60S ribosomal protein L7a (chains CG)
MAPKRGGKAPVPAKKKTDKVTNPLFEKRPKQFGIGGALPPKKDLHRFVKWPKVVRIQRQR
RILKQRLKVPPALHQFTRTLDKNLATNLFKMLLKYRPEDKAAKKERLLKRAQAEAEGKTV
EAKKPIVVKYGLNHVTYLIEQSKAQLVVIAHDVDPIELVVWLPALCRKMEVPYCIVKGKS
RLGSIVHKKTASVLCLTTVKNEDKLEFSKILEAIKANFNDKFDEVRKKWGGGVMGSKSQA
KTKARERLIAKEAAQRMN
Sequence of entity 11 (CH), FASTA
>8JIV_11 Ribosomal protein L6 alpha-beta domain-containing protein (chains CH)
MKTILASETMEIPEEVTVKVSAKMISVTGPRGTLTRNFKHLNLDFQLQEGGRKLKVDAWF
GTRKTMAAIRTAISHVQNLITGVTKGFRYKMRFVYAHFPINASITAANKGIEIRNFLGEK
KVRKVDMLDGVTILRSEKVKDEIVLDGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYV
SDKGAIKEE
Sequence of entity 12 (CI), FASTA
>8JIV_12 Ribosomal protein L10e/L16 domain-containing protein (chains CI)
MGRRPARCYRQIKNKPYPKSRYCRGVPDPKIRIYDVGMKKKGVDEFPSCVHLVSWEKENV
SSEALEAARIACNKYMTKNAGKDAFHLRVRVHPYHVLRINKMLSCAGADRLQTGMRGAFG
KPLGTCARVDIGQVLLSVRCKESNAVHADEALRRAKFKFPGRQKIIRSRKWGFTKFNRAD
YIKYKSEGRIVPDGVNAKLLGVHGPIAKRAPGQAILA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg242
ZNZinc ionZn3

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

Primary citation

Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Mishra, R.K., Sharma, P., Khaja, F.T. et al. Structure (2024) 32:562. DOI 10.1016/j.str.2024.02.006 · PubMed

Other PDB entries of the same protein (UniProt W5ECL2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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