5LZT: UL2

Name: PDB 5LZT: Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.
Published: 2016-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the mammalian ribosomal termination complex with eRF1 and eRF3. Determined by electron microscopy at 3.65 Å resolution. Released 30 Nov 2016.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 87
Atoms: 222,683
Mol. weight: 3544.78 kDa
Ligands: GCP, ZN, MG
Released: 30 Nov 2016

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

Secondary structure: helices and β-sheets

5LZT contains 575 α-helices and 622 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	8-11	4
α-helix	42-48	7
β-strand	72-73	2	193
α-helix	75-77	3
α-helix	79-81	3
α-helix	84-92	9
β-strand	97	1	117
α-helix	98-99	2
β-strand	100-102	3	194
β-strand	110-111	2	193
α-helix	116-118	3
β-strand	123-126	4	194
α-helix	131-140	10
β-strand	144-146	3	194

Chain A: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-11	6
β-strand	18	1	1
α-helix	19	1
α-helix	28-32	5
α-helix	34-38	5
β-strand	40-41	2	2
β-strand	43-49	7	3
α-helix	57	1
β-strand	58-63	6	3
β-strand	73-77	5	3
β-strand	79	1	4
β-strand	82-83	2	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	174-176	3
α-helix	182-192	11
β-strand	193	1	1
α-helix	201-203	3
β-strand	224-225	2	7
β-strand	237-238	2	7

Chain aa: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	197
β-strand	29-31	3	197
β-strand	36-38	3	198
β-strand	43	1	199
α-helix	48-56	9
β-strand	57	1	132
α-helix	63-65	3
β-strand	66	1	199
β-strand	71-73	3	198
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain AA: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	195
β-strand	38-41	4	195
β-strand	47-49	3	195
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	196
α-helix	81-83	3
α-helix	84-94	11
β-strand	97-100	4	196
β-strand	121-124	4	196
α-helix	131-139	9
β-strand	144-148	5	196
β-strand	159-162	4	196
α-helix	168-184	17
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	51-53	3
α-helix	55-75	21
α-helix	91-100	10
α-helix	106-116	11

Chain B: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	27-28	2
α-helix	40-41	2
β-strand	43	1	14
β-strand	45-54	10	15
β-strand	56-59	4	16
β-strand	71-73	3	16
β-strand	76-80	5	15
α-helix	82-83	2
β-strand	84-92	9	17
β-strand	101-106	6	17
α-helix	112-115	4
α-helix	131-134	4
α-helix	135-137	3
α-helix	140-155	16
β-strand	159-165	7	17
β-strand	182-184	3	17
β-strand	185	1	14
α-helix	190-199	10
β-strand	204-205	2	17
α-helix	207-210	4
β-strand	216-222	7	15
α-helix	223-225	3
β-strand	228-229	2	18
α-helix	231-235	5
α-helix	238-241	4
α-helix	262-263	2
β-strand	270-271	2	18
β-strand	276-278	3	15
β-strand	282-288	7	15
β-strand	292-293	2	19
β-strand	298-299	2	19
β-strand	320	1	20
β-strand	324	1	20
β-strand	330-335	6	15
β-strand	344-349	6	15
α-helix	361-363	3
β-strand	365-368	4	16
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	10
β-strand	36	1	11
β-strand	44-47	4	10
β-strand	55	1	12
α-helix	57-59	3
β-strand	62	1	12
β-strand	64-65	2	13
α-helix	71	1
β-strand	72-73	2	13
α-helix	74	1
β-strand	78	1	11
β-strand	81	1	10

Chain BB: 11 helices, 11 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	58-62	5
β-strand	66	1	8
β-strand	69-70	2	8
α-helix	71-74	4
β-strand	82-90	9	8
β-strand	95-105	11	8
α-helix	107-113	7
β-strand	120-128	9	8
β-strand	134-142	9	8
β-strand	143	1	9
α-helix	144-146	3
α-helix	155-157	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
α-helix	201-203	3
β-strand	207	1	9
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

>5LZT_1 uL2 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (B), FASTA

>5LZT_2 uL3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (C), FASTA

>5LZT_3 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA

Sequence of entity 4 (D), FASTA

>5LZT_4 uL18 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (E), FASTA

>5LZT_5 eL6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 6 (F), FASTA

>5LZT_6 uL30 (chains F)
MEGAEEKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEY
RQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGT
FVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGK
YNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQIN
RLIRRMN

Sequence of entity 7 (G), FASTA

>5LZT_7 eL8 (chains G)
MSSYRLGYCMKEERHNLVLCLWSQSPGILNSKCLWPFTNIHLLVGALPREGAGGAWGGGR
SEQLPTCSTTHHDFTWDKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQR
AILYKRLKVPPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGD
VPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGK
ARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSV
ARIAKLEKAKAKELATKLG

Sequence of entity 8 (H), FASTA

>5LZT_8 uL6 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 9 (I), FASTA

>5LZT_9 uL16 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>5LZT_10 uL5 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 11 (L), FASTA

>5LZT_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>5LZT_12 eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	282

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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