6W6L: Human ribosome-TMCO1 translocon
Cryo-EM structure of the human ribosome-TMCO1 translocon. Determined by electron microscopy at 3.84 Å resolution. Released 2 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.84 Å
- Organism
- Homo sapiens
- Chains
- 54
- Atoms
- 148,773
- Mol. weight
- 2349.79 kDa
- Ligands
- ZN, MG
- Released
- 2 Sept 2020
Explore 6W6L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6W6L contains 348 α-helices and 314 β-strands across 49 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: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 17-21 | 5 | |
| α-helix | 29-45 | 17 | |
| α-helix | 62-68 | 7 | |
| α-helix | 82-96 | 15 | |
| α-helix | 106-132 | 27 | |
| α-helix | 146-148 | 3 | |
| α-helix | 151-170 | 20 | |
| α-helix | 178-195 | 18 | |
| α-helix | 213-222 | 10 | |
| α-helix | 226-234 | 9 | |
| α-helix | 242-260 | 19 | |
| β-strand | 262-269 | 8 | 83 |
| β-strand | 276-282 | 7 | 83 |
| α-helix | 285-288 | 4 | |
| α-helix | 289-311 | 23 | |
| α-helix | 342-345 | 4 | |
| α-helix | 358-382 | 25 | |
| α-helix | 387-396 | 10 | |
| β-strand | 399-401 | 3 | 83 |
| α-helix | 406-408 | 3 | |
| α-helix | 409-438 | 30 | |
| α-helix | 445-464 | 20 | |
Chain 2: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| β-strand | 26 | 1 | 83 |
| α-helix | 27-28 | 2 | |
| α-helix | 30-67 | 38 | |
Chain 3: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-94 | 23 | |
Chain 4: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 32-56 | 25 | |
| α-helix | 65-69 | 5 | |
| α-helix | 70-89 | 20 | |
| α-helix | 90-92 | 3 | |
| α-helix | 96-124 | 29 | |
| α-helix | 129-158 | 30 | |
| α-helix | 161-163 | 3 | |
| α-helix | 166-177 | 12 | |
| α-helix | 179-189 | 11 | |
| α-helix | 196-220 | 25 | |
Chain 5: 20 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 45-47 | 3 | 96 |
| α-helix | 49 | 1 | |
| β-strand | 50 | 1 | 97 |
| α-helix | 51 | 1 | |
| β-strand | 62 | 1 | 97 |
| β-strand | 85-88 | 4 | 96 |
| α-helix | 94-102 | 9 | |
| β-strand | 108-111 | 4 | 96 |
| β-strand | 143-146 | 4 | 96 |
| α-helix | 149-164 | 16 | |
| α-helix | 170-171 | 2 | |
| β-strand | 175 | 1 | 98 |
| β-strand | 218-223 | 6 | 99 |
| α-helix | 232-234 | 3 | |
| α-helix | 238-242 | 5 | |
| α-helix | 243-257 | 15 | |
| α-helix | 259 | 1 | |
| α-helix | 260-262 | 3 | |
| β-strand | 269-274 | 6 | 99 |
| α-helix | 284-293 | 10 | |
| β-strand | 307-311 | 5 | 99 |
| β-strand | 319-324 | 6 | 99 |
| α-helix | 332-338 | 7 | |
| α-helix | 340-348 | 9 | |
| β-strand | 358-361 | 4 | 99 |
| α-helix | 372-377 | 6 | |
| β-strand | 382-386 | 5 | 99 |
| α-helix | 403-405 | 3 | |
| α-helix | 408-431 | 24 | |
| α-helix | 449-456 | 8 | |
| α-helix | 457-461 | 5 | |
| α-helix | 475-486 | 12 | |
| β-strand | 513 | 1 | 98 |
| α-helix | 524-557 | 34 | |
Chain 6: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-30 | 24 | |
| α-helix | 33-56 | 24 | |
| α-helix | 63-107 | 45 | |
| α-helix | 123-129 | 7 | |
| α-helix | 143-162 | 20 | |
| α-helix | 166-172 | 7 | |
Chain 7: 13 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 161-178 | 18 | |
| α-helix | 197-200 | 4 | |
| β-strand | 207-208 | 2 | 6 |
| β-strand | 218-220 | 3 | 6 |
| α-helix | 230-236 | 7 | |
| β-strand | 244-249 | 6 | 6 |
| α-helix | 250-252 | 3 | |
| α-helix | 255-258 | 4 | |
| β-strand | 261-264 | 4 | 6 |
| α-helix | 266-275 | 10 | |
| α-helix | 277-281 | 5 | |
| β-strand | 300-303 | 4 | 6 |
| α-helix | 306-311 | 6 | |
| α-helix | 315-324 | 10 | |
| β-strand | 330-332 | 3 | 6 |
| β-strand | 359-364 | 6 | 6 |
| α-helix | 377-379 | 3 | |
| α-helix | 380-395 | 16 | |
| α-helix | 400-445 | 46 | |
| α-helix | 450-473 | 24 | |
Chain a: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-13 | 5 | 5 |
| β-strand | 23-29 | 7 | 5 |
| β-strand | 40-48 | 9 | 5 |
| α-helix | 49-52 | 4 | |
| α-helix | 59-64 | 6 | |
| β-strand | 69-76 | 8 | 5 |
| α-helix | 77-79 | 3 | |
| β-strand | 80-86 | 7 | 5 |
| α-helix | 104-122 | 19 | |
| α-helix | 128-131 | 4 | |
| α-helix | 133-134 | 2 | |
41 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 |
|---|
| 60S ribosomal protein L8 | A | protein | 257 | Homo sapiens | P62917 (AlphaFold model) |
| 60S ribosomal protein L3 | B | protein | 403 | Homo sapiens | P39023 (AlphaFold model) |
| 60S ribosomal protein L4 | C | protein | 427 | Homo sapiens | P36578 (AlphaFold model) |
| 5.8S ribosomal RNA | D | RNA | 157 | Homo sapiens | |
| 5S ribosomal RNA | E | RNA | 119 | Homo sapiens | |
| 60S ribosomal protein L5 | F | protein | 297 | Homo sapiens | P46777 (AlphaFold model) |
| 60S ribosomal protein L6 | G | protein | 288 | Homo sapiens | Q02878 |
| 60S ribosomal protein L7 | H | protein | 248 | Homo sapiens | P18124 |
| 60S ribosomal protein L7a | I | protein | 266 | Homo sapiens | P62424 |
| 60S ribosomal protein L9 | J | protein | 192 | Homo sapiens | P32969 |
| 60S ribosomal protein L10 | K | protein | 214 | Homo sapiens | P27635 |
| 60S ribosomal protein L11 | L | protein | 178 | Homo sapiens | P62913 |
42 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6W6L_1 60S ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>6W6L_2 60S ribosomal protein L3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 3 (C), FASTA
>6W6L_3 60S ribosomal protein L4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 4 (D), FASTA
>6W6L_4 5.8S ribosomal RNA (chains D)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
Sequence of entity 5 (E), FASTA
>6W6L_5 5S ribosomal RNA (chains E)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCU
Sequence of entity 6 (F), FASTA
>6W6L_6 60S ribosomal protein L5 (chains F)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 7 (G), FASTA
>6W6L_7 60S ribosomal protein L6 (chains G)
MAGEKVEKPDTKEKKPEAKKVDAGGKVKKGNLKAKKPKKGKPHCSRNPVLVRGIGRYSRS
AMYSRKAMYKRKYSAAKSKVEKKKKEKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTED
VPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLASGLLLVTGPLV
LNRVPLRRTHQKFVIATSTKIDISNVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKY
EITEQRKIDQKAVDSQILPKIKAIPQLQGYLRSVFALTNGIYPHKLVF
Sequence of entity 8 (H), FASTA
>6W6L_8 60S ribosomal protein L7 (chains H)
MEGVEEKKKEVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKE
YRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNG
TFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLG
KYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQI
NRLIRRMN
Sequence of entity 9 (I), FASTA
>6W6L_9 60S ribosomal protein L7a (chains I)
MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRY
IRLQRQRAILYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEK
KAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVP
YCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGN
VLGPKSVARIAKLEKAKAKELATKLG
Sequence of entity 10 (J), FASTA
>6W6L_10 60S ribosomal protein L9 (chains J)
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 11 (K), FASTA
>6W6L_11 60S ribosomal protein L10 (chains K)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 12 (L), FASTA
>6W6L_12 60S ribosomal protein L11 (chains L)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| MG | Magnesium ion | Mg | 28 |
Primary citation
An ER translocon for multi-pass membrane protein biogenesis. McGilvray, P.T., Anghel, S.A., Sundaram, A. et al. Elife (2020) 9. DOI 10.7554/eLife.56889 · PubMed
Other PDB entries of the same protein (UniProt P62917 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
- 29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
- 8QYX 1.78 Å, Human 60S ribosomal subunit
- 8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
- 9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
- 8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
- 9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
- 29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
- 9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
- 9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
- 9PBE 2.19 Å, In situ human 80S ribosome (composite map)
- 29IX 2.2 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. NT-2 added to purified…
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