6YBD: PDB entry 6YBD
Structure of a human 48S translational initiation complex - eIF3. Determined by electron microscopy at 3.3 Å resolution. Released 16 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Homo sapiens
- Chains
- 19
- Atoms
- 30,742
- Mol. weight
- 797.99 kDa
- Released
- 16 Sept 2020
Explore 6YBD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YBD contains 224 α-helices and 101 β-strands across 19 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 3: 17 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-16 | 14 | |
| α-helix | 19-21 | 3 | |
| α-helix | 23-25 | 3 | |
| α-helix | 26-38 | 13 | |
| α-helix | 45-56 | 12 | |
| α-helix | 58-60 | 3 | |
| α-helix | 63-74 | 12 | |
| α-helix | 81-87 | 7 | |
| α-helix | 93-95 | 3 | |
| α-helix | 97-110 | 14 | |
| α-helix | 114-120 | 7 | |
| α-helix | 126-129 | 4 | |
| α-helix | 138-149 | 12 | |
| β-strand | 153 | 1 | 31 |
| α-helix | 155-161 | 7 | |
| α-helix | 167-177 | 11 | |
| β-strand | 180-181 | 2 | 31 |
| β-strand | 187-188 | 2 | 31 |
| α-helix | 192-195 | 4 | |
| α-helix | 207-215 | 9 | |
Chain 4: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 91-93 | 3 | 1 |
| α-helix | 96-105 | 10 | |
| β-strand | 118-122 | 5 | 2 |
| β-strand | 128-130 | 3 | 1 |
| β-strand | 133-135 | 3 | 2 |
| α-helix | 150-163 | 14 | |
| β-strand | 168-174 | 7 | 2 |
| α-helix | 181-193 | 13 | |
| β-strand | 199-202 | 4 | 2 |
| β-strand | 213-214 | 2 | 2 |
| α-helix | 245-254 | 10 | |
| α-helix | 266-289 | 24 | |
| α-helix | 301-303 | 3 | |
| α-helix | 306-314 | 9 | |
| α-helix | 320-352 | 33 | |
Chain 5: 18 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 184-206 | 23 | |
| α-helix | 209-217 | 9 | |
| α-helix | 224-246 | 23 | |
| α-helix | 253-256 | 4 | |
| α-helix | 257-262 | 6 | |
| α-helix | 263-267 | 5 | |
| α-helix | 275-289 | 15 | |
| α-helix | 298-302 | 5 | |
| α-helix | 312-325 | 14 | |
| α-helix | 329-334 | 6 | |
| α-helix | 336-341 | 6 | |
| α-helix | 358-374 | 17 | |
| α-helix | 388-400 | 13 | |
| α-helix | 406-416 | 11 | |
| α-helix | 439-461 | 23 | |
| β-strand | 469-470 | 2 | 32 |
| α-helix | 472-480 | 9 | |
| α-helix | 491-496 | 6 | |
| β-strand | 504-506 | 3 | 32 |
| β-strand | 513-515 | 3 | 32 |
| α-helix | 527-548 | 22 | |
Chain 6: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-24 | 7 | |
| α-helix | 31-34 | 4 | |
| α-helix | 64-67 | 4 | |
| α-helix | 88-91 | 4 | |
| α-helix | 99-105 | 7 | |
| α-helix | 106-108 | 3 | |
| α-helix | 117-127 | 11 | |
| α-helix | 155-167 | 13 | |
| α-helix | 175-192 | 18 | |
| α-helix | 199-211 | 13 | |
| α-helix | 252-256 | 5 | |
| α-helix | 263-266 | 4 | |
| α-helix | 269-277 | 9 | |
| α-helix | 281-284 | 4 | |
| α-helix | 297-300 | 4 | |
| α-helix | 308-317 | 10 | |
| α-helix | 342-345 | 4 | |
| α-helix | 348-354 | 7 | |
Chain 8: 14 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 7 |
| α-helix | 43-50 | 8 | |
| β-strand | 65-71 | 7 | 7 |
| β-strand | 75-80 | 6 | 7 |
| β-strand | 83 | 1 | 7 |
| α-helix | 98-104 | 7 | |
| β-strand | 116-122 | 7 | 7 |
| α-helix | 132-143 | 12 | |
| β-strand | 148-152 | 5 | 7 |
| β-strand | 164-166 | 3 | 7 |
| β-strand | 167-169 | 3 | 8 |
| α-helix | 171-175 | 5 | |
| β-strand | 198-200 | 3 | 8 |
| α-helix | 212-223 | 12 | |
| α-helix | 229-234 | 6 | |
| α-helix | 235-240 | 6 | |
| α-helix | 248-272 | 25 | |
| α-helix | 273-278 | 6 | |
| α-helix | 281 | 1 | |
| α-helix | 282-287 | 6 | |
| α-helix | 306-308 | 3 | |
| α-helix | 316-350 | 35 | |
Chain G: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-30 | 13 | |
| β-strand | 51-52 | 2 | 9 |
| β-strand | 58-59 | 2 | 9 |
| β-strand | 60-65 | 6 | 10 |
| α-helix | 66-69 | 4 | |
| α-helix | 78-86 | 9 | |
| β-strand | 92-97 | 6 | 10 |
| α-helix | 114-117 | 4 | |
| α-helix | 130-133 | 4 | |
| β-strand | 142-146 | 5 | 11 |
| β-strand | 152-157 | 6 | 11 |
| α-helix | 170-181 | 12 | |
| β-strand | 185-188 | 4 | 11 |
Chain H: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| β-strand | 32-36 | 5 | 12 |
| β-strand | 43-47 | 5 | 12 |
| β-strand | 55 | 1 | 13 |
| β-strand | 62 | 1 | 13 |
| β-strand | 64-65 | 2 | 14 |
| β-strand | 72-73 | 2 | 14 |
| β-strand | 78 | 1 | 12 |
| β-strand | 79 | 1 | 15 |
Chain I: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-40 | 9 | |
| α-helix | 49-56 | 8 | |
| α-helix | 63-67 | 5 | |
| α-helix | 72-75 | 4 | |
| α-helix | 86-89 | 4 | |
| α-helix | 97-102 | 6 | |
| α-helix | 111-114 | 4 | |
| α-helix | 123-129 | 7 | |
| α-helix | 146-149 | 4 | |
11 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 |
|---|
| Eukaryotic translation initiation factor 3 subunit M | 6 | protein | 374 | Homo sapiens | Q7L2H7 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit F | 4 | protein | 357 | Homo sapiens | O00303 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit A | u | protein | 1382 | Homo sapiens | Q14152 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit E | v | protein | 445 | Homo sapiens | P60228 (AlphaFold model) |
| Eukaryotic translation initiation factor 3 subunit C | y | protein | 913 | Homo sapiens | Q99613 |
| Eukaryotic translation initiation factor 3 subunit H | 8 | protein | 352 | Homo sapiens | O15372 |
| 40S ribosomal protein S7 | G | protein | 194 | Homo sapiens | P62081 |
| 40S ribosomal protein S27 | H | protein | 84 | Homo sapiens | P42677 |
| 40S ribosomal protein S21 | K | protein | 83 | Homo sapiens | P63220 |
| 40S ribosomal protein S17 | M | protein | 135 | Homo sapiens | P08708 |
| 40S ribosomal protein S2 | L | protein | 293 | Homo sapiens | P15880 |
| 40S ribosomal protein S3a | O | protein | 264 | Homo sapiens | P61247 |
7 more molecules are not listed.
Sequence of entity 1 (6), FASTA
>6YBD_1 Eukaryotic translation initiation factor 3 subunit M (chains 6)
MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDV
ESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVR
YTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDA
ASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDL
LTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQE
LQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQN
LNKVKNSLLSLSDT
Sequence of entity 2 (4), FASTA
>6YBD_2 Eukaryotic translation initiation factor 3 subunit F (chains 4)
MATPAVPVSAPPATPTPVPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPG
QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTL
LGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDIT
EHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYA
YYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA
DNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
Sequence of entity 3 (u), FASTA
>6YBD_3 Eukaryotic translation initiation factor 3 subunit A (chains u)
MPAYFQRPENALKRANEFLEVGKKQPALDVLYDVMKSKKHRTWQKIHEPIMLKYLELCVD
LRKSHLAKEGLYQYKNICQQVNIKSLEDVVRAYLKMAEEKTEAAKEESQQMVLDIEDLDN
IQTPESVLLSAVSGEDTQDRTDRLLLTPWVKFLWESYRQCLDLLRNNSRVERLYHDIAQQ
AFKFCLQYTRKAEFRKLCDNLRMHLSQIQRHHNQSTAINLNNPESQSMHLETRLVQLDSA
ISMELWQEAFKAVEDIHGLFSLSKKPPKPQLMANYYNKVSTVFWKSGNALFHASTLHRLY
HLSREMRKNLTQDEMQRMSTRVLLATLSIPITPERTDIARLLDMDGIIVEKQRRLATLLG
LQAPPTRIGLINDMVRFNVLQYVVPEVKDLYNWLEVEFNPLKLCERVTKVLNWVREQPEK
EPELQQYVPQLQNNTILRLLQQVSQIYQSIEFSRLTSLVPFVDAFQLERAIVDAARHCDL
QVRIDHTSRTLSFGSDLNYATREDAPIGPHLQSMPSEQIRNQLTAMSSVLAKALEVIKPA
HILQEKEEQHQLAVTAYLKNSRKEHQRILARRQTIEERKERLESLNIQREKEELEQREAE
LQKVRKAEEERLRQEAKEREKERILQEHEQIKKKTVRERLEQIKKTELGAKAFKDIDIED
LEELDPDFIMAKQVEQLEKEKKELQERLKNQEKKIDYFERAKRLEEIPLIKSAYEEQRIK
DMDLWEQQEEERITTMQLEREKALEHKNRMSRMLEDRDLFVMRLKAARQSVYEEKLKQFE
ERLAEERHNRLEERKRQRKEERRITYYREKEEEEQRRAEEQMLKEREERERAERAKREEE
LREYQERVKKLEEVERKKRQRELEIEERERRREEERRLGDSSLSRKDSRWGDRDSEGTWR
KGPEADSEWRRGPPEKEWRRGEGRDEDRSHRRDEERPRRLGDDEDREPSLRPDDDRVPRR
GMDDDRGPRRGPEEDRFSRRGADDDRPSWRNTDDDRPPRRIADEDRGNWRHADDDRPPRR
GLDEDRGSWRTADEDRGPRRGMDDDRGPRRGGADDERSSWRNADDDRGPRRGLDDDRGPR
RGMDDDRGPRRGMDDDRGPRRGMDDDRGPRRGLDDDRGPWRNADDDRIPRRGAEDDRGPW
RNMDDDRLSRRADDDRFPRRGDDSRPGPWRPLVKPGGWREKEKAREESWGPPRESRPSEE
REWDREKERDRDNQDREENDKDPERERDRERDVDREDRFRRPRDEGGWRRGPAEESSSWR
DSSRRDDRDRDDRRRERDDRRDLRERRDLRDDRDRRGPPLRSEREEVSSWRRADDRKDDR
VEERDPPRRVPPPALSRDRERDRDREREGEKEKASWRAEKDRESLRRTKNETDEDGWTTV
RR
Sequence of entity 4 (v), FASTA
>6YBD_4 Eukaryotic translation initiation factor 3 subunit E (chains v)
MAEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKN
LYSDDIPHALREKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTRDGRMLFDYLADK
HGFRQEYLDTLYRYAKFQYECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQ
NWDAAMEDLTRLKETIDNNSVSSPLQSLQQRTWLIHWSLFVFFNHPKGRDNIIDLFLYQP
QYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQESYTYKDPITEFVECLY
VNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISINMLADKL
NMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAM
NIEKKLNQNSRSEAPNWATQDSGFY
Sequence of entity 5 (y), FASTA
>6YBD_5 Eukaryotic translation initiation factor 3 subunit C (chains y)
MSRFFTTGSDSESESSLSGEELVTKPVGGNYGKQPLLLSEDEEDTKRVVRSAKDKRFEEL
TNLIRTIRNAMKIRDVTKCLEEFELLGKAYGKAKSIVDKEGVPRFYIRILADLEDYLNEL
WEDKEGKKKMNKNNAKALSTLRQKIRKYNRDFESHITSYKQNPEQSADEDAEKNEEDSEG
SSDEDEDEDGVSAATFLKKKSEAPSGESRKFLKKMDDEDEDSEDSEDDEDWDTGSTSSDS
DSEEEEGKQTALASRFLKKAPTTDEDKKAAEKKREDKAKKKHDRKSKRLDEEEEDNEGGE
WERVRGGVPLVKEKPKMFAKGTEITHAVVIKKLNEILQARGKKGTDRAAQIELLQLLVQI
AAENNLGEGVIVKIKFNIIASLYDYNPNLATYMKPEMWGKCLDCINELMDILFANPNIFV
GENILEESENLHNADQPLRVRGCILTLVERMDEEFTKIMQNTDPHSQEYVEHLKDEAQVC
AIIERVQRYLEEKGTTEEVCRIYLLRILHTYYKFDYKAHQRQLTPPEGSSKSEQDQAENE
GEDSAVLMERLCKYIYAKDRTDRIRTCAILCHIYHHALHSRWYQARDLMLMSHLQDNIQH
ADPPVQILYNRTMVQLGICAFRQGLTKDAHNALLDIQSSGRAKELLGQGLLLRSLQERNQ
EQEKVERRRQVPFHLHINLELLECVYLVSAMLLEIPYMAAHESDARRRMISKQFHHQLRV
GERQPLLGPPESMREHVVAASKAMKMGDWKTCHSFIINEKMNGKVWDLFPEADKVRTMLV
RKIQEESLRTYLFTYSSVYDSISMETLSDMFELDLPTVHSIISKMIINEELMASLDQPTQ
TVVMHRTEPTAQQNLALQLAEKLGSLVENNERVFDHKQGTYGGYFRDQKDGYRKNEGYMR
RGGYRQQQSQTAY
Sequence of entity 6 (8), FASTA
>6YBD_6 Eukaryotic translation initiation factor 3 subunit H (chains 8)
MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGT
EVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWY
QSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEK
DFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLG
KNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEED
LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN
Sequence of entity 7 (G), FASTA
>6YBD_7 40S ribosomal protein S7 (chains G)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL
Sequence of entity 8 (H), FASTA
>6YBD_8 40S ribosomal protein S27 (chains H)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH
Sequence of entity 9 (K), FASTA
>6YBD_9 40S ribosomal protein S21 (chains K)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF
Sequence of entity 10 (M), FASTA
>6YBD_10 40S ribosomal protein S17 (chains M)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV
Sequence of entity 11 (L), FASTA
>6YBD_11 40S ribosomal protein S2 (chains L)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
Sequence of entity 12 (O), FASTA
>6YBD_12 40S ribosomal protein S3a (chains O)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Primary citation
Structure of a human 48Stranslational initiation complex. Brito Querido, J., Sokabe, M., Kraatz, S. et al. Science (2020) 369:1220-1227. DOI 10.1126/science.aba4904 · PubMed
Other PDB entries of the same protein (UniProt Q7L2H7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
- 28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
- 6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
- 8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
- 8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
- 28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
- 6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
- 9KZU 3.0 Å, Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome…
- 8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
- 9KN5 3.2 Å, Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
- 9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
- 9KKF 3.3 Å, Structure of the human 40S ribosome complexed with HCV IRES and eIF3
Browse structure collections
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