5LZU: UL2

Name: PDB 5LZU: Structure of the mammalian ribosomal termination complex with accommodated eRF1
Published: 2016-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the mammalian ribosomal termination complex with accommodated eRF1. Determined by electron microscopy at 3.75 Å resolution. Released 30 Nov 2016.

Method: Electron microscopy
Resolution: 3.75 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 85
Atoms: 219,122
Mol. weight: 3473.14 kDa
Ligands: ZN, MG
Released: 30 Nov 2016

Explore 5LZU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LZU contains 562 α-helices and 615 β-strands across 78 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
α-helix	44-47	4
α-helix	65-68	4
β-strand	73	1	196
α-helix	84-92	9
β-strand	98	1	116
α-helix	99	1
β-strand	100-102	3	197
α-helix	104-106	3
β-strand	110-111	2	196
β-strand	122-125	4	197
β-strand	128-129	2	196
α-helix	131-140	10
β-strand	142-145	4	197

Chain A: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-12	7
β-strand	18	1	1
α-helix	30-32	3
α-helix	34-37	4
β-strand	41-50	10	2
α-helix	51	1
β-strand	57-64	8	2
β-strand	71-77	7	2
α-helix	78	1
β-strand	79	1	3
β-strand	83	1	4
β-strand	87-90	4	2
β-strand	101-103	3	2
β-strand	112-114	3	2
β-strand	116	1	5
β-strand	126	1	5
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	3
α-helix	182-189	8
β-strand	193	1	1
α-helix	201-203	3
β-strand	224-225	2	6
β-strand	237-238	2	6

Chain aa: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	193
β-strand	29-31	3	193
β-strand	36-40	5	194
β-strand	43	1	195
α-helix	48-56	9
β-strand	57	1	122
β-strand	66	1	195
β-strand	69-73	5	194
α-helix	75-80	6
α-helix	91-93	3
α-helix	96-99	4

Chain AA: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	190
α-helix	34-36	3
β-strand	38-41	4	190
α-helix	42	1
β-strand	47-49	3	190
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	191
α-helix	84-94	11
β-strand	97-100	4	191
β-strand	121-124	4	191
α-helix	131-139	9
β-strand	144-148	5	191
β-strand	159-162	4	191
α-helix	168-185	18
β-strand	187	1	192
β-strand	189	1	192
α-helix	194-195	2
α-helix	199-201	3
α-helix	207-217	11

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
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: 18 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	40-41	2
β-strand	43	1	12
β-strand	45-50	6	13
β-strand	54	1	13
β-strand	57-59	3	14
β-strand	63	1	15
β-strand	65	1	15
β-strand	71-73	3	14
β-strand	76-80	5	13
α-helix	82-83	2
β-strand	84-94	11	16
β-strand	99-106	8	16
α-helix	112-116	5
α-helix	131-134	4
α-helix	135-138	4
α-helix	140-155	16
β-strand	159-165	7	16
α-helix	168-170	3
α-helix	177-179	3
β-strand	180-184	5	16
β-strand	185	1	12
α-helix	190-200	11
β-strand	204-205	2	16
α-helix	207-210	4
β-strand	216-217	2	17
β-strand	220-222	3	13
α-helix	223-225	3
β-strand	228-229	2	18
α-helix	231-235	5
α-helix	237-241	5
α-helix	262-263	2
β-strand	270-271	2	18
β-strand	276-278	3	13
β-strand	282-283	2	17
β-strand	284-288	5	13
β-strand	292-293	2	19
β-strand	298-299	2	19
α-helix	316	1
β-strand	320	1	20
β-strand	324	1	20
β-strand	330-335	6	13
β-strand	344-348	5	13
β-strand	349	1	17
α-helix	361-363	3
β-strand	365	1	14
α-helix	382-389	8

Chain bb: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-35	4	201
β-strand	36	1	202
β-strand	44-47	4	201
β-strand	55	1	203
α-helix	56	1
α-helix	57-59	3
β-strand	62	1	203
β-strand	64-65	2	204
α-helix	71	1
β-strand	72-73	2	204
α-helix	74	1
β-strand	78	1	202
β-strand	81	1	201

Chain BB: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	28-34	7	198
β-strand	43-50	8	198
α-helix	51-52	2
β-strand	53	1	199
β-strand	56	1	199
α-helix	58-62	5
β-strand	66	1	198
β-strand	69-70	2	198
α-helix	71-74	4
β-strand	82-91	10	198
β-strand	96-105	10	198
α-helix	107-113	7
β-strand	120-128	9	198
β-strand	134-142	9	198
β-strand	143	1	200
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	200
β-strand	211-219	9	198
α-helix	225-231	7

70 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)
60S ribosomal protein L5	D	protein	297	Oryctolagus cuniculus	P19949 (AlphaFold model)
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7
uL30	F	protein	247	Oryctolagus cuniculus	G1SV32
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

73 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5LZU_1 uL2 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (B), FASTA

>5LZU_2 uL3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (C), FASTA

>5LZU_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA

Sequence of entity 4 (D), FASTA

>5LZU_4 60S ribosomal protein L5 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (E), FASTA

>5LZU_5 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 6 (F), FASTA

>5LZU_6 uL30 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN

Sequence of entity 7 (G), FASTA

>5LZU_7 eL8 (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG

Sequence of entity 8 (H), FASTA

>5LZU_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 9 (I), FASTA

>5LZU_9 uL16 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>5LZU_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 11 (L), FASTA

>5LZU_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>5LZU_12 eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	258

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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