6SWA: Mus musculus brain neocortex ribosome 60S
Mus musculus brain neocortex ribosome 60S bound to Ebp1. Determined by electron microscopy at 3.1 Å resolution. Released 30 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Mus musculus
- Chains
- 46
- Atoms
- 138,160
- Mol. weight
- 2043.92 kDa
- Ligands
- ZN, MG
- Released
- 30 Sept 2020
Explore 6SWA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6SWA contains 293 α-helices and 316 β-strands across 43 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: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-23 | 10 | |
| β-strand | 26-29 | 4 | 6 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-48 | 4 | 6 |
| α-helix | 54-67 | 14 | |
| β-strand | 70-73 | 4 | 6 |
| α-helix | 78-85 | 8 | |
| β-strand | 93-98 | 6 | 6 |
Chain A: 9 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 9-12 | 4 | |
| α-helix | 30-32 | 3 | |
| α-helix | 34-37 | 4 | |
| β-strand | 40-49 | 10 | 1 |
| α-helix | 50-51 | 2 | |
| β-strand | 58-64 | 7 | 1 |
| β-strand | 71-77 | 7 | 1 |
| β-strand | 79 | 1 | 2 |
| β-strand | 82-83 | 2 | 3 |
| β-strand | 87-91 | 5 | 1 |
| β-strand | 101-103 | 3 | 1 |
| β-strand | 112-116 | 5 | 1 |
| β-strand | 126 | 1 | 1 |
| β-strand | 134-136 | 3 | 1 |
| β-strand | 140 | 1 | 4 |
| β-strand | 145 | 1 | 4 |
| β-strand | 146-149 | 4 | 1 |
| β-strand | 155-158 | 4 | 1 |
| β-strand | 163-166 | 4 | 1 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 2 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-192 | 11 | |
| β-strand | 225 | 1 | 5 |
| α-helix | 229-230 | 2 | |
| β-strand | 238 | 1 | 5 |
Chain b: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-28 | 7 | 11 |
| α-helix | 29-32 | 4 | |
| α-helix | 38-40 | 3 | |
| α-helix | 42-56 | 15 | |
| β-strand | 61-64 | 4 | 11 |
| α-helix | 66-72 | 7 | |
| α-helix | 73-75 | 3 | |
| β-strand | 83-92 | 10 | 11 |
| β-strand | 102-108 | 7 | 11 |
| β-strand | 121-122 | 2 | 11 |
Chain B: 13 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-35 | 4 | |
| β-strand | 45-53 | 9 | 7 |
| β-strand | 56-59 | 4 | 8 |
| β-strand | 71-74 | 4 | 8 |
| β-strand | 76-80 | 5 | 7 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-95 | 12 | 9 |
| β-strand | 98-105 | 8 | 9 |
| α-helix | 112-115 | 4 | |
| α-helix | 116-118 | 3 | |
| α-helix | 135-138 | 4 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 9 |
| α-helix | 168-170 | 3 | |
| β-strand | 180-184 | 5 | 9 |
| α-helix | 190-199 | 10 | |
| β-strand | 204-205 | 2 | 9 |
| α-helix | 207-210 | 4 | |
| β-strand | 216-222 | 7 | 7 |
| β-strand | 225-229 | 5 | 10 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-240 | 4 | |
| β-strand | 270-273 | 4 | 10 |
| β-strand | 276-288 | 13 | 7 |
| β-strand | 330-335 | 6 | 7 |
| β-strand | 344-349 | 6 | 7 |
| α-helix | 353-354 | 2 | |
| β-strand | 364-368 | 5 | 8 |
| α-helix | 382-389 | 8 | |
Chain c: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 19-20 | 2 | |
| α-helix | 44-47 | 4 | |
| α-helix | 53-56 | 4 | |
| α-helix | 58-60 | 3 | |
| α-helix | 61-63 | 3 | |
| β-strand | 75-79 | 5 | 14 |
| α-helix | 86-89 | 4 | |
| β-strand | 95-99 | 5 | 14 |
| α-helix | 105-118 | 14 | |
| β-strand | 122 | 1 | 14 |
Chain C: 24 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 12 |
| β-strand | 17-23 | 7 | 12 |
| α-helix | 24-25 | 2 | |
| α-helix | 26-29 | 4 | |
| α-helix | 34-45 | 12 | |
| α-helix | 49-51 | 3 | |
| β-strand | 64-65 | 2 | 13 |
| β-strand | 78-79 | 2 | 13 |
| β-strand | 90 | 1 | 13 |
| α-helix | 100-101 | 2 | |
| α-helix | 104-106 | 3 | |
| α-helix | 117-130 | 14 | |
| α-helix | 134-138 | 5 | |
| β-strand | 152-154 | 3 | 12 |
| α-helix | 158-160 | 3 | |
| α-helix | 165-173 | 9 | |
| α-helix | 177-185 | 9 | |
| α-helix | 189-191 | 3 | |
| α-helix | 193-195 | 3 | |
| β-strand | 208-211 | 4 | 12 |
| α-helix | 217-220 | 4 | |
| β-strand | 228-231 | 4 | 12 |
| α-helix | 237-240 | 4 | |
| α-helix | 242-244 | 3 | |
| β-strand | 250-253 | 4 | 12 |
| α-helix | 254-258 | 5 | |
| α-helix | 260-263 | 4 | |
| α-helix | 279-281 | 3 | |
| α-helix | 289-294 | 6 | |
| α-helix | 296-299 | 4 | |
| α-helix | 312-317 | 6 | |
| α-helix | 325-328 | 4 | |
| α-helix | 331-359 | 29 | |
Chain d: 3 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 21 |
| β-strand | 7 | 1 | 18 |
| β-strand | 9-16 | 8 | 18 |
| β-strand | 21-30 | 10 | 18 |
| α-helix | 36-41 | 6 | |
| β-strand | 46-57 | 12 | 18 |
| β-strand | 65-77 | 13 | 18 |
| β-strand | 84-88 | 5 | 18 |
| α-helix | 91-93 | 3 | |
| α-helix | 94-96 | 3 | |
| β-strand | 100 | 1 | 18 |
| β-strand | 102-103 | 2 | 18 |
Chain D: 15 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-15 | 6 | |
| α-helix | 21-24 | 4 | |
| α-helix | 32-36 | 5 | |
| β-strand | 50-56 | 7 | 15 |
| β-strand | 59-66 | 8 | 15 |
| β-strand | 73-78 | 6 | 15 |
| α-helix | 83-86 | 4 | |
| α-helix | 95-113 | 19 | |
| α-helix | 139-141 | 3 | |
| β-strand | 143 | 1 | 16 |
| β-strand | 145-147 | 3 | 15 |
| α-helix | 158-169 | 12 | |
| β-strand | 172 | 1 | 16 |
| β-strand | 183 | 1 | 17 |
| β-strand | 190 | 1 | 17 |
| α-helix | 192-199 | 8 | |
| α-helix | 203-214 | 12 | |
| α-helix | 216-221 | 6 | |
| α-helix | 224-228 | 5 | |
| α-helix | 236-249 | 14 | |
| α-helix | 254-257 | 4 | |
| α-helix | 268-271 | 4 | |
| α-helix | 273-296 | 24 | |
35 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 | 252 | Mus musculus | P62918 (AlphaFold model) |
| 60S ribosomal protein L3 | B | protein | 394 | Mus musculus | P27659 (AlphaFold model) |
| 60S ribosomal protein L4 | C | protein | 363 | Mus musculus | Q9D8E6 (AlphaFold model) |
| 60S ribosomal protein L5 | D | protein | 294 | Mus musculus | P47962 (AlphaFold model) |
| 60S ribosomal protein L6 | E | protein | 194 | Mus musculus | P47911 |
| 60S ribosomal protein L7 | F | protein | 234 | Mus musculus | P14148 |
| 60S ribosomal protein L7a | G | protein | 234 | Mus musculus | P12970 |
| 60S ribosomal protein L9 | H | protein | 191 | Mus musculus | P51410 |
| 60S ribosomal protein L10 | I | protein | 211 | Mus musculus | Q6ZWV3 |
| 60S ribosomal protein L11 | J | protein | 169 | Mus musculus | Q9CXW4 |
| 60S ribosomal protein L13 | K | protein | 205 | Mus musculus | P47963 |
| 60S ribosomal protein L14 | L | protein | 139 | Mus musculus | Q9CR57 |
34 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6SWA_1 60S ribosomal protein L8 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGTKTVQ
Sequence of entity 2 (B), FASTA
>6SWA_2 60S ribosomal protein L3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKD
Sequence of entity 3 (C), FASTA
>6SWA_3 60S ribosomal protein L4 (chains C)
CARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQT
SAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRY
AICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVQLLKKLKAWNDIKK
VYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAP
GGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMMNTDLSRILKSPEIQRAL
RAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVKKLEAAATALA
TKS
Sequence of entity 4 (D), FASTA
>6SWA_4 60S ribosomal protein L5 (chains D)
VKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQ
IAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQV
EVNGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGY
DSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKA
HAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>6SWA_5 60S ribosomal protein L6 (chains E)
TVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRRLRSSITPGTVLIILT
GRHRGKRVVFLKQLDSGLLLVTGPLVINRVPLRRTHQKFVIATSTKVDISDVKIPKHLTD
AYFKKKQLRKPRHQEGEIFDTEKEKYEITEQRKADQKAVDLQILPKIKAVPQLQGYLRSQ
FSLTNGMYPHKLVF
Sequence of entity 6 (F), FASTA
>6SWA_6 60S ribosomal protein L7 (chains F)
PETLKKKRRNFAELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARM
ARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLR
IVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNSLIARSLGKFGIICMEDLIHEI
YTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
Sequence of entity 7 (G), FASTA
>6SWA_7 60S ribosomal protein L7a (chains G)
NPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQALD
RQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTLVE
NKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGHLVHRKTCTTVAFTQVN
SEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELA
Sequence of entity 8 (H), FASTA
>6SWA_8 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVEITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRTGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQAD
Sequence of entity 9 (I), FASTA
>6SWA_9 60S ribosomal protein L10 (chains I)
RRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSS
EALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKP
QGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFE
DMVAEKRLIPDGCGVKYIPNRGPLDKWRALH
Sequence of entity 10 (J), FASTA
>6SWA_10 60S ribosomal protein L11 (chains J)
ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKI
AVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGL
DFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG
Sequence of entity 11 (K), FASTA
>6SWA_11 60S ribosomal protein L13 (chains K)
APSRNGMILKPHFHKDWQQRVDTWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQD
Sequence of entity 12 (L), FASTA
>6SWA_12 60S ribosomal protein L14 (chains L)
VFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNR
IIKTEVKKLQRAAILKASP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| MG | Magnesium ion | Mg | 247 |
Primary citation
Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Kraushar, M.L., Krupp, F., Harnett, D. et al. Mol Cell (2021) 81:304. DOI 10.1016/j.molcel.2020.11.037 · PubMed
Other PDB entries of the same protein (UniProt P62918 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9H4N 2.46 Å, RPL13 (eL13)-mutant 80S ribosome from mouse
- 31FX 2.54 Å, Mouse 80S ribosome, sgRNA control
- 31FY 2.57 Å, Mouse 80S ribosome, Gm10076 KO
- 9KDT 2.63 Å, Cryo-EM structure of 80S ribosome
- 9KDW 2.67 Å, Cryo-EM structure of 80S ribosome
- 9QOH 2.78 Å, Mouse Ribosome POST translocation state
- 9QQP 2.8 Å, Mouse Ribosome rotated-2 PRE state
- 7CPU 2.82 Å, Cryo-EM structure of 80S ribosome from mouse kidney
- 31FZ 2.89 Å, Mouse 80S ribosome, eL41 KO
- 9KDU 2.96 Å, Cryo-EM structure of 80S ribosome
- 7CPV 3.03 Å, Cryo-EM structure of 80S ribosome from mouse testis
- 9QQL 3.09 Å, Mouse RPS15 P131 Mutant Ribosome POST translocation state
Browse structure collections
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