5LZV: UL2
Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1. Determined by electron microscopy at 3.35 Å resolution. Released 30 Nov 2016.
- Method
- Electron microscopy
- Resolution
- 3.35 Å
- Organisms
- Oryctolagus cuniculus, Homo sapiens
- Chains
- 87
- Atoms
- 223,874
- Mol. weight
- 3544.08 kDa
- Ligands
- MG, ZN, SF4
- Released
- 30 Nov 2016
Explore 5LZV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5LZV contains 595 α-helices and 629 β-strands across 79 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: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
| α-helix | 42-48 | 7 | |
| β-strand | 72-74 | 3 | 203 |
| α-helix | 75-77 | 3 | |
| α-helix | 84-92 | 9 | |
| β-strand | 98 | 1 | 128 |
| α-helix | 99 | 1 | |
| β-strand | 100-102 | 3 | 204 |
| α-helix | 103-106 | 4 | |
| β-strand | 110-112 | 3 | 203 |
| β-strand | 122-126 | 5 | 204 |
| β-strand | 128-129 | 2 | 203 |
| α-helix | 131-140 | 10 | |
| β-strand | 142-146 | 5 | 204 |
Chain A: 9 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 14-16 | 3 | |
| β-strand | 18 | 1 | 1 |
| α-helix | 29-32 | 4 | |
| α-helix | 34-37 | 4 | |
| β-strand | 40-41 | 2 | 2 |
| β-strand | 43-49 | 7 | 3 |
| α-helix | 50-51 | 2 | |
| α-helix | 57 | 1 | |
| β-strand | 58-63 | 6 | 3 |
| β-strand | 73-77 | 5 | 3 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 4 |
| β-strand | 83 | 1 | 5 |
| β-strand | 87 | 1 | 3 |
| β-strand | 90-91 | 2 | 2 |
| β-strand | 101-103 | 3 | 2 |
| β-strand | 112-114 | 3 | 2 |
| β-strand | 116 | 1 | 6 |
| β-strand | 126 | 1 | 6 |
| β-strand | 134-140 | 7 | 2 |
| β-strand | 145-149 | 5 | 2 |
| β-strand | 155-159 | 5 | 2 |
| β-strand | 163-166 | 4 | 2 |
| α-helix | 168 | 1 | |
| β-strand | 169 | 1 | 4 |
| α-helix | 182-192 | 11 | |
| β-strand | 193 | 1 | 1 |
| β-strand | 224-225 | 2 | 7 |
| β-strand | 237-238 | 2 | 7 |
Chain aa: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 207 |
| β-strand | 29-31 | 3 | 207 |
| β-strand | 36-40 | 5 | 208 |
| β-strand | 43 | 1 | 209 |
| α-helix | 48-56 | 9 | |
| β-strand | 66 | 1 | 209 |
| β-strand | 69-73 | 5 | 208 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
| α-helix | 96-99 | 4 | |
Chain AA: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-21 | 10 | |
| β-strand | 25 | 1 | 205 |
| α-helix | 34-36 | 3 | |
| β-strand | 38-41 | 4 | 205 |
| α-helix | 42 | 1 | |
| β-strand | 47-49 | 3 | 205 |
| α-helix | 51-67 | 17 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 206 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 206 |
| β-strand | 121-124 | 4 | 206 |
| α-helix | 131-139 | 9 | |
| β-strand | 144-148 | 5 | 206 |
| β-strand | 159-162 | 4 | 206 |
| α-helix | 168-185 | 18 | |
| α-helix | 194-195 | 2 | |
| α-helix | 199-202 | 4 | |
| α-helix | 207-217 | 11 | |
Chain b: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-19 | 8 | |
| α-helix | 22-24 | 3 | |
| α-helix | 37-48 | 12 | |
| α-helix | 49-51 | 3 | |
| α-helix | 55-75 | 21 | |
| α-helix | 91-100 | 10 | |
| α-helix | 106-116 | 11 | |
Chain B: 17 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| α-helix | 32-35 | 4 | |
| β-strand | 42-43 | 2 | 15 |
| β-strand | 45-54 | 10 | 16 |
| β-strand | 57-59 | 3 | 17 |
| β-strand | 71-73 | 3 | 17 |
| β-strand | 76-80 | 5 | 16 |
| α-helix | 82-83 | 2 | |
| β-strand | 84-92 | 9 | 18 |
| β-strand | 101-106 | 6 | 18 |
| α-helix | 112-115 | 4 | |
| α-helix | 116-118 | 3 | |
| α-helix | 131-134 | 4 | |
| α-helix | 135-138 | 4 | |
| α-helix | 140-156 | 17 | |
| β-strand | 159-165 | 7 | 18 |
| α-helix | 178-179 | 2 | |
| β-strand | 180-184 | 5 | 18 |
| β-strand | 185-186 | 2 | 15 |
| α-helix | 190-199 | 10 | |
| β-strand | 204-205 | 2 | 18 |
| α-helix | 207-210 | 4 | |
| β-strand | 216-222 | 7 | 16 |
| α-helix | 223-225 | 3 | |
| β-strand | 228-229 | 2 | 19 |
| α-helix | 231-234 | 4 | |
| α-helix | 237-240 | 4 | |
| α-helix | 262-263 | 2 | |
| β-strand | 270-271 | 2 | 19 |
| β-strand | 276-286 | 11 | 16 |
| β-strand | 292-293 | 2 | 20 |
| β-strand | 298-299 | 2 | 20 |
| β-strand | 320 | 1 | 21 |
| β-strand | 324 | 1 | 21 |
| β-strand | 330-334 | 5 | 16 |
| β-strand | 344-349 | 6 | 16 |
| α-helix | 361-363 | 3 | |
| β-strand | 365-367 | 3 | 17 |
| α-helix | 382-389 | 8 | |
Chain bb: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| β-strand | 32-35 | 4 | 11 |
| β-strand | 36 | 1 | 12 |
| β-strand | 44-47 | 4 | 11 |
| β-strand | 55 | 1 | 13 |
| α-helix | 57-59 | 3 | |
| β-strand | 62 | 1 | 13 |
| β-strand | 64-65 | 2 | 14 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 14 |
| α-helix | 74 | 1 | |
| β-strand | 78 | 1 | 12 |
| β-strand | 81 | 1 | 11 |
Chain BB: 11 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 28-34 | 7 | 8 |
| β-strand | 43-50 | 8 | 8 |
| α-helix | 51-52 | 2 | |
| β-strand | 53 | 1 | 9 |
| β-strand | 56 | 1 | 9 |
| α-helix | 58-62 | 5 | |
| β-strand | 66 | 1 | 8 |
| β-strand | 69-70 | 2 | 8 |
| α-helix | 71-74 | 4 | |
| β-strand | 82-91 | 10 | 8 |
| β-strand | 96-105 | 10 | 8 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-128 | 9 | 8 |
| β-strand | 134-142 | 9 | 8 |
| β-strand | 143 | 1 | 10 |
| α-helix | 144-146 | 3 | |
| α-helix | 155-157 | 3 | |
| α-helix | 158-177 | 20 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 207 | 1 | 10 |
| β-strand | 211-219 | 9 | 8 |
| α-helix | 225-231 | 7 | |
71 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 |
|---|
| uL2 | A | protein | 257 | Oryctolagus cuniculus | G1TT27 (AlphaFold model) |
| uL3 | B | protein | 403 | Oryctolagus cuniculus | G1TL06 (AlphaFold model) |
| uL4 | C | protein | 425 | Oryctolagus cuniculus | G1SVW5 (AlphaFold model) |
| uL18 | D | protein | 297 | Oryctolagus cuniculus | P19949 (AlphaFold model) |
| eL6 | E | protein | 291 | Oryctolagus cuniculus | G1SKF7 |
| uL30 | F | protein | 247 | Oryctolagus cuniculus | G1TUB1 |
| eL8 | G | protein | 319 | Oryctolagus cuniculus | G1STW0 |
| uL6 | H | protein | 192 | Oryctolagus cuniculus | G1SWI6 |
| uL16 | I | protein | 214 | Oryctolagus cuniculus | B7NZQ2 |
| uL5 | J | protein | 178 | Oryctolagus cuniculus | G1TUB8 |
| eL13 | L | protein | 211 | Oryctolagus cuniculus | |
| eL14 | M | protein | 218 | Oryctolagus cuniculus | G1SZ12 |
75 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5LZV_1 uL2 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 2 (B), FASTA
>5LZV_2 uL3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 3 (C), FASTA
>5LZV_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA
Sequence of entity 4 (D), FASTA
>5LZV_4 uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 5 (E), FASTA
>5LZV_5 eL6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 6 (F), FASTA
>5LZV_6 uL30 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN
Sequence of entity 7 (G), FASTA
>5LZV_7 eL8 (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG
Sequence of entity 8 (H), FASTA
>5LZV_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 9 (I), FASTA
>5LZV_9 uL16 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS
Sequence of entity 10 (J), FASTA
>5LZV_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK
Sequence of entity 11 (L), FASTA
>5LZV_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Sequence of entity 12 (M), FASTA
>5LZV_12 eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 300 |
| ZN | Zinc ion | Zn | 8 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Primary citation
Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Shao, S., Murray, J., Brown, A. et al. Cell (2016) 167:1229-1240.e15. DOI 10.1016/j.cell.2016.10.046 · PubMed
Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
- 8SCB 2.5 Å, Terminating ribosome with SRI-41315
- 9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
- 9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
- 8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
- 8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
- 8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
- 6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
- 7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
- 9BDL 2.8 Å, 80S ribosome with angiogenin
- 9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
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