3E1Y: Human eRF1/eRF3 complex

Crystal structure of human eRF1/eRF3 complex. Determined by X-ray diffraction at 3.8 Å resolution. Released 19 May 2009.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,110
Mol. weight: 294.13 kDa
Ligands: ATP
Released: 19 May 2009

Explore 3E1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E1Y contains 60 α-helices and 164 β-strands across 8 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.

Chains A and B: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-22	15
β-strand	34-39	6	1
α-helix	45-58	14
α-helix	65-82	18
β-strand	93-99	7	1
α-helix	103-105	3
β-strand	109-114	6	1
β-strand	123-128	6	1
α-helix	136-139	4
α-helix	143-144	2
β-strand	145-151	7	2
β-strand	156-162	7	2
β-strand	165-172	8	2
α-helix	187-212	26
β-strand	214	1	3
β-strand	219	1	3
β-strand	225-228	4	2
α-helix	233-236	4
α-helix	244-248	5
β-strand	252-255	4	2
α-helix	260-269	10
α-helix	272-275	4
α-helix	278-294	17
β-strand	301-303	3	4
α-helix	306-313	8
β-strand	317-323	7	4
β-strand	329	1	5
β-strand	373	1	5
α-helix	374-379	6
α-helix	383-385	3
β-strand	389-392	4	4
α-helix	397-405	9
β-strand	409-413	5	4

Chain C: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	11-25	15
β-strand	36-38	3	10
α-helix	48-56	9
α-helix	68-81	14
β-strand	94-96	3	10
β-strand	113-114	2	10
β-strand	124-126	3	10
α-helix	136-138	3
β-strand	148-151	4	11
β-strand	156-159	4	11
β-strand	162	1	12
β-strand	165	1	12
β-strand	170-172	3	11
α-helix	199-212	14
β-strand	214	1	13
β-strand	219	1	13
β-strand	225-228	4	11
β-strand	239	1	14
β-strand	242	1	14
α-helix	244-247	4
β-strand	253-255	3	11
α-helix	260-275	16
α-helix	278-292	15
β-strand	301	1	15
α-helix	305-313	9
β-strand	319	1	15
β-strand	322	1	16
β-strand	323	1	17
β-strand	329-330	2	18
β-strand	345-346	2	18
β-strand	372-373	2	18
α-helix	374-379	6
β-strand	392	1	17
α-helix	397-404	8
β-strand	409	1	16
β-strand	412	1	15

Chain D: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	11-25	15
β-strand	36-38	3	19
α-helix	48-56	9
α-helix	68-81	14
β-strand	94-96	3	19
β-strand	113-114	2	19
β-strand	124-126	3	19
α-helix	137-140	4
β-strand	148-151	4	20
β-strand	156-159	4	20
β-strand	162	1	21
β-strand	165	1	21
β-strand	170-172	3	20
α-helix	199-212	14
β-strand	214	1	22
β-strand	219	1	22
β-strand	225-228	4	20
β-strand	239	1	23
β-strand	242	1	23
α-helix	244-247	4
β-strand	253-255	3	20
α-helix	260-275	16
α-helix	278-292	15
β-strand	301	1	24
α-helix	305-313	9
β-strand	319	1	24
β-strand	322	1	25
β-strand	323	1	26
β-strand	329-330	2	27
β-strand	345-346	2	27
β-strand	372-373	2	27
α-helix	374-379	6
β-strand	392	1	26
α-helix	397-404	8
β-strand	409	1	25
β-strand	412	1	24

Chains E and F: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	441	1	28
β-strand	442-443	2	29
β-strand	444-450	7	30
β-strand	452-458	7	30
β-strand	461	1	28
β-strand	464-465	2	31
β-strand	470-472	3	30
β-strand	477-484	8	30
β-strand	491	1	30
β-strand	493-494	2	31
β-strand	499-506	8	30
β-strand	517-518	2	29
β-strand	519	1	30
β-strand	530-536	7	32
β-strand	548-553	6	32
β-strand	558-566	9	32
β-strand	590-597	8	32
α-helix	610-612	3
β-strand	614-618	5	32
β-strand	625-632	8	32

Chains G and H: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	441	1	38
β-strand	442-443	2	39
β-strand	446-450	5	39
β-strand	452-458	7	39
β-strand	461	1	38
β-strand	464-465	2	40
β-strand	470-472	3	39
β-strand	478-483	6	39
β-strand	484	1	41
β-strand	486	1	39
β-strand	491	1	41
β-strand	493-494	2	40
β-strand	499-506	8	39
β-strand	517-519	3	39
β-strand	526-537	12	42
β-strand	548-553	6	42
β-strand	560-563	4	42
β-strand	566-568	3	42
α-helix	581-582	2
β-strand	591-603	13	42
α-helix	610-612	3
β-strand	614-618	5	42
β-strand	625-632	8	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic peptide chain release factor subunit 1	A, B, C, D	protein	451	Homo sapiens	P62495 (AlphaFold model)
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	E, F, G, H	protein	204	Homo sapiens	P15170 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3E1Y_1 Eukaryotic peptide chain release factor subunit 1 (chains A, B, C, D)
MRGSHHHHHHGMASMADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQIS
RVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGK
EKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTR
EVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAVQLFISGDKVNVAGLVL
AGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKL
IGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYL
TPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGF
GGIGGILRYRVDFQGMEYQGGDDEFFDLDDY

Sequence of entity 2 (E, F, G, H), FASTA

>3E1Y_2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains E, F, G, H)
GPLGSPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDT
VAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLH
IHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMG
RFTLRDEGKTIAIGKVLKLVPEKD

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structural insights into eRF3 and stop codon recognition by eRF1. Cheng, Z., Saito, K., Pisarev, A.V. et al. Genes Dev (2009) 23:1106-1118. DOI 10.1101/gad.1770109 · 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

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