3J5Y: PDB entry 3J5Y

Structure of the mammalian ribosomal pre-termination complex associated with eRF1-eRF3-GDPNP. Determined by electron microscopy at 9.7 Å resolution. Released 25 Dec 2013.

Method: Electron microscopy
Resolution: 9.7 Å
Organisms: Homo sapiens, Oryctolagus cuniculus
Chains: 4
Atoms: 8,724
Mol. weight: 126.08 kDa
Released: 25 Dec 2013

Explore 3J5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J5Y contains 31 α-helices and 46 β-strands across 2 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: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
β-strand	28	1	1
β-strand	34-39	6	2
α-helix	45-58	14
α-helix	65-82	18
β-strand	93-102	10	2
α-helix	103-105	3
β-strand	106-114	9	2
β-strand	124-128	5	2
β-strand	130	1	1
α-helix	134-140	7
β-strand	145-151	7	3
β-strand	155-162	8	3
β-strand	165-173	9	3
α-helix	187-212	26
β-strand	214-215	2	4
β-strand	218-219	2	4
β-strand	224-228	5	3
α-helix	234-237	4
α-helix	246-248	3
β-strand	250-255	6	3
α-helix	262-269	8
α-helix	272-274	3
α-helix	281-294	14
β-strand	301-303	3	5
α-helix	306-313	8
β-strand	317-323	7	5
β-strand	329-334	6	6
α-helix	335	1
β-strand	341-346	6	6
α-helix	348-352	5
β-strand	367-373	7	6
α-helix	374-379	6
β-strand	386-392	7	5
α-helix	397-401	5
α-helix	402-406	5
β-strand	409-413	5	5

Chain B: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	211-219	9	7
α-helix	225-234	10
α-helix	241-253	13
α-helix	257-259	3
α-helix	262-264	3
α-helix	269-274	6
β-strand	281-286	6	7
β-strand	290-296	7	7
α-helix	304-312	9
β-strand	316-322	7	7
α-helix	327-331	5
α-helix	338-347	10
β-strand	353-358	6	7
α-helix	369-387	19
β-strand	394-398	5	7
α-helix	422-428	7
β-strand	441-450	10	8
β-strand	452-458	7	8
β-strand	469-472	4	8
β-strand	478-486	9	8
β-strand	489-491	3	8
β-strand	499-505	7	8
α-helix	512-513	2
β-strand	514	1	9
β-strand	516	1	9
β-strand	517-519	3	8
β-strand	527	1	10
β-strand	530-537	8	11
β-strand	544	1	12
β-strand	549-554	6	11
β-strand	557-570	14	11
α-helix	576	1
β-strand	577	1	11
α-helix	578	1
β-strand	585	1	12
β-strand	590-597	8	11
β-strand	602	1	10
α-helix	610-612	3
β-strand	614-618	5	11
β-strand	625-633	9	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic peptide chain release factor subunit 1	A	protein	414	Homo sapiens	P62495 (AlphaFold model)
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	B	protein	428	Homo sapiens	P15170 (AlphaFold model)
5'-r(apupupgpupapapapapa)-3'	C	RNA	10	Homo sapiens
tRNA-Leu	D	RNA	88	Oryctolagus cuniculus

Sequence of entity 1 (A), FASTA

>3J5Y_1 Eukaryotic peptide chain release factor subunit 1 (chains A)
AADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRV
NRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYL
CDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQS
ALRFARLRMEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRL
QSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVE
DTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEH
ELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQ

Sequence of entity 2 (B), FASTA

>3J5Y_2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains B)
APKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKEKNRETWYLSWALD
TNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
EFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSIERYEECKEKLVPFLKKV
GFSPKKDIHFMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNLPNFNRSIDGPIRLPIVD
KYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKG
IEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITAL
ICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAI
GKVLKLVP

Sequence of entity 3 (C), FASTA

>3J5Y_3 5'-R(*AP*UP*UP*GP*UP*AP*AP*AP*AP*A)-3' (chains C)
AUUGUAAAAA

Sequence of entity 4 (D), FASTA

>3J5Y_4 tRNA-Leu (chains D)
GCGGGGGUUGCCGAGCCUGGUCAAAGGCGGGGGACUCAAGAUCCCCUCCCGUAGGGGUUC
CGGGGUUCGAAUCCCCGCCCCCGCACCA

Primary citation

Structure of the mammalian ribosomal pre-termination complex associated with eRF1*eRF3*GDPNP. des Georges, A., Hashem, Y., Unbehaun, A. et al. Nucleic Acids Res (2014) 42:3409-3418. DOI 10.1093/nar/gkt1279 · PubMed

Other PDB entries of the same protein (UniProt P62495 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
9S3D 2.32 Å, NAC bound human RNC with 58 amino acid ARF1-linker
9S3B 2.38 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1
9S3C 2.42 Å, NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
1DT9 2.7 Å, The crystal structure of human eukaryotic release factor ERF1-mechanism of stop codon…
9QLP 2.75 Å, NMT1-NAC bound human RNC with full length ARF1 - State 2
6XA1 2.8 Å, Structure of a drug-like compound stalled human translation termination complex

Browse structure collections

About this viewer

MolViewer shows 3J5Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.