7QP6: Human 48S initiation complex in open state

Structure of the human 48S initiation complex in open state (h48S AUG open). Determined by electron microscopy at 4.7 Å resolution. Released 11 May 2022.

Method
Electron microscopy
Resolution
4.7 Å
Organism
Homo sapiens
Chains
53
Atoms
109,900
Mol. weight
2140.66 kDa
Ligands
MG, ZN
Released
11 May 2022

Explore 7QP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QP6 contains 443 α-helices and 393 β-strands across 50 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: 7 helices, 39 β-strands

ElementResiduesLengthSheet
α-helix287-2915
α-helix295-2984
β-strand309-31021
β-strand315-31951
β-strand328-33251
β-strand338-34252
β-strand348-35362
β-strand356-36162
β-strand366-37272
β-strand378-38143
β-strand387-39153
β-strand404-40853
β-strand414-41853
β-strand430-43124
β-strand438-44254
β-strand445-45064
β-strand455-45624
α-helix460-4634
β-strand469-47245
β-strand479-48355
α-helix4901
β-strand491-49665
β-strand50315
β-strand507-50935
β-strand515-51956
β-strand525-53176
β-strand542-54876
β-strand556-56166
β-strand565-57067
α-helix5711
β-strand576-58167
α-helix584-5863
β-strand587-59487
β-strand600-609107
β-strand613-61538
β-strand62319
β-strand624-62638
β-strand63819
β-strand639110
β-strand644110
β-strand656-659411
β-strand666-669411
β-strand680-683411
β-strand692-695411
β-strand70111
α-helix704-7063
Chain 3: 17 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix3-1513
α-helix19-213
α-helix23-253
α-helix26-3813
α-helix44-5613
α-helix58-603
α-helix63-7412
α-helix81-877
α-helix91-944
α-helix97-11014
α-helix114-1207
α-helix126-1294
α-helix138-14912
β-strand152-153218
α-helix155-1617
α-helix167-17711
β-strand180118
β-strand187-188218
α-helix192-1954
α-helix207-2159
Chain 4: 8 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand93120
α-helix96-10813
β-strand118-122521
β-strand130120
β-strand133-135321
α-helix150-16314
β-strand168-173621
α-helix181-19010
β-strand198-202522
β-strand213-217522
α-helix245-25511
α-helix266-28924
α-helix301-3033
α-helix306-3149
α-helix320-35233
Chain 5: 18 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix184-20623
α-helix209-2179
α-helix223-24624
α-helix253-2553
α-helix256-2627
α-helix263-2675
α-helix275-28915
α-helix298-3025
α-helix312-32514
α-helix329-3346
α-helix336-3416
α-helix358-37417
α-helix388-40013
α-helix406-41611
α-helix439-46022
α-helix472-4809
α-helix491-4966
β-strand504-505226
β-strand514-515226
α-helix527-54822
Chain 6: 17 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix18-247
α-helix30-323
α-helix64-674
α-helix88-903
α-helix99-1057
α-helix106-1083
α-helix117-12711
α-helix155-16713
α-helix175-19117
α-helix199-21113
α-helix263-2664
α-helix269-2779
α-helix282-2854
α-helix297-3004
α-helix308-31710
β-strand322128
β-strand332128
α-helix342-3454
α-helix348-3547
Chain 8: 15 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix33-353
β-strand38-39234
α-helix43-508
β-strand65-68435
β-strand71134
β-strand75-76234
β-strand80135
α-helix98-1047
β-strand116-122735
α-helix131-14313
β-strand148-152535
β-strand165-166235
β-strand167-169336
α-helix171-1755
β-strand198-200336
α-helix212-22312
α-helix225-2273
α-helix229-2346
α-helix235-2406
α-helix248-27326
α-helix274-2785
α-helix2811
α-helix282-2876
α-helix306-3083
α-helix316-35035
Chain 9: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix3-2119
Chain a: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix5-1814
β-strand20-24533
α-helix34-363
α-helix42-5514
β-strand58-62533
β-strand66-71633
α-helix73-8311

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Eukaryotic translation initiation factor 3 subunit B1protein813Homo sapiensP55884 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit K3protein218Homo sapiensQ9UBQ5 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit F4protein357Homo sapiensO00303 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit L5protein564Homo sapiensQ9Y262 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit M6protein374Homo sapiensQ7L2H7
mRNA7RNA20Homo sapiens
Eukaryotic translation initiation factor 3 subunit H8protein352Homo sapiensO15372
60S ribosomal protein L419protein25Homo sapiensP62945
18S rRNAARNA1869Homo sapiens
40S ribosomal protein S11Bprotein158Homo sapiensP62280
40S ribosomal protein S4, X isoformCprotein263Homo sapiensP62701
40S ribosomal protein S9Dprotein194Homo sapiensP46781

41 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>7QP6_1 Eukaryotic translation initiation factor 3 subunit B (chains 1)
MQDAENVAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAGTEASSEEVGIAEA
GPESEVRTEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQARDERSDSR
AQAVSEDAGGNEGRAAEAEPRALENGDADEPSFSDPEDFVDDVSEEELLGDVLKDRPQEA
DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP
AHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMTISDEWDIPEKQPFKDLGNLRYWLEEA
ECRDQYSVIFESGDRTSIFWNDVKDPVSIEERARWTETYVRWSPKGTYLATFHQRGIALW
GGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQAIIIWDILTGHKKRGFHC
ESSAHWPIFKWSHDGKFFARMTLDTLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA
FWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDRTPKGTQGV
VTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKNNGKI
ELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWD
PTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQI
KKDLKKYSKIFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMEQKNERLELRG
GVDTDELDSNVDDWEEETIEFFVTEEIIPLGNQ
Sequence of entity 2 (3), FASTA
>7QP6_2 Eukaryotic translation initiation factor 3 subunit K (chains 3)
MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAF
FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA
LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWS
ADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMASSQ
Sequence of entity 3 (4), FASTA
>7QP6_3 Eukaryotic translation initiation factor 3 subunit F (chains 4)
MATPAVPVSAPPATPTPVPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPG
QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTL
LGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDIT
EHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYA
YYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA
DNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
Sequence of entity 4 (5), FASTA
>7QP6_4 Eukaryotic translation initiation factor 3 subunit L (chains 5)
MSYPADDYESEAAYDPYAYPSDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFH
KTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAP
QVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPN
QWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNI
NRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELN
KKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMI
NKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKF
LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLD
LTEQEFRIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYG
DFFIRQIHKFEELNRTLKKMGQRP
Sequence of entity 5 (6), FASTA
>7QP6_5 Eukaryotic translation initiation factor 3 subunit M (chains 6)
MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDV
ESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVR
YTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDA
ASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDL
LTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQE
LQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQN
LNKVKNSLLSLSDT
Sequence of entity 6 (7), FASTA
>7QP6_6 mRNA (chains 7)
AAAAAAAAAAAAAAAAAAAA
Sequence of entity 7 (8), FASTA
>7QP6_7 Eukaryotic translation initiation factor 3 subunit H (chains 8)
MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGT
EVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWY
QSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEK
DFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLG
KNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEED
LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN
Sequence of entity 8 (9), FASTA
>7QP6_8 60S ribosomal protein L41 (chains 9)
MRAKWRKKRMRRLKRKRRKMRQRSK
Sequence of entity 9 (A), FASTA
>7QP6_9 18S rRNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUG
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA
Sequence of entity 10 (B), FASTA
>7QP6_10 40S ribosomal protein S11 (chains B)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF
Sequence of entity 11 (C), FASTA
>7QP6_11 40S ribosomal protein S4, X isoform (chains C)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG
Sequence of entity 12 (D), FASTA
>7QP6_12 40S ribosomal protein S9 (chains D)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg2
ZNZinc ionZn2

Primary citation

Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. Yi, S.H., Petrychenko, V., Schliep, J.E. et al. Nucleic Acids Res (2022) 50:5282-5298. DOI 10.1093/nar/gkac283 · PubMed

Other PDB entries of the same protein (UniProt P55884 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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