5IZL: Human eEFSec

The crystal structure of human eEFSec in complex with GDPCP. Determined by X-ray diffraction at 2.72 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,350
Mol. weight: 136.22 kDa
Ligands: GCP, MG
Released: 12 Oct 2016

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

Secondary structure: helices and β-sheets

5IZL contains 37 α-helices and 77 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: 18 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	1
α-helix	20-30	11
β-strand	52-59	8	1
α-helix	60-61	2
α-helix	62-67	6
α-helix	82-84	3
β-strand	85-92	8	1
α-helix	93-94	2
α-helix	97-99	3
α-helix	100-107	8
β-strand	112-118	7	1
α-helix	125-137	13
β-strand	140-146	7	1
α-helix	156-170	15
β-strand	181-183	3	1
β-strand	185	1	2
β-strand	200	1	2
α-helix	202-212	11
β-strand	225-233	9	3
β-strand	239-247	9	3
β-strand	249-251	3	4
β-strand	255-258	4	3
β-strand	263-272	10	3
β-strand	275-276	2	3
β-strand	279-281	3	4
β-strand	285-290	6	3
α-helix	295-297	3
β-strand	301-304	4	3
β-strand	310-317	8	5
β-strand	319	1	6
β-strand	320-321	2	5
β-strand	330	1	7
β-strand	334-339	6	5
β-strand	342-347	6	5
β-strand	350-353	4	8
α-helix	355-357	3
α-helix	361-362	2
β-strand	372-376	5	8
β-strand	378	1	7
β-strand	410	1	6
β-strand	411-412	2	8
β-strand	413-422	10	5
β-strand	427-431	5	5
β-strand	444-454	11	5
α-helix	459-462	4
α-helix	464-466	3
β-strand	468-477	10	8
β-strand	478-481	4	9
β-strand	487-488	2	8
β-strand	489-491	3	9
α-helix	500-503	4
β-strand	507-510	4	8
β-strand	515-518	4	8
β-strand	530-531	2	8
α-helix	538-542	5
β-strand	575-582	8	8
α-helix	586-588	3
β-strand	593	1	8

Chain B: 19 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	10
α-helix	20-30	11
β-strand	52-59	8	10
α-helix	60-61	2
α-helix	62-64	3
β-strand	85-92	8	10
α-helix	97-99	3
α-helix	100-106	7
β-strand	112-118	7	10
β-strand	122	1	10
α-helix	125-137	13
β-strand	140-146	7	10
α-helix	148-150	3
α-helix	153-171	19
β-strand	181-183	3	10
β-strand	185	1	11
α-helix	198-199	2
β-strand	200	1	11
α-helix	202-212	11
β-strand	225-234	10	12
β-strand	238-247	10	12
β-strand	251	1	13
β-strand	255-258	4	12
α-helix	259-261	3
β-strand	263-272	10	12
β-strand	275-277	3	12
β-strand	279	1	13
β-strand	285-290	6	12
α-helix	295-297	3
β-strand	301-304	4	12
β-strand	310-317	8	14
β-strand	319	1	15
β-strand	320-321	2	14
β-strand	330	1	16
β-strand	334-339	6	14
β-strand	342-353	12	14
α-helix	355-357	3
α-helix	361-362	2
β-strand	372-375	4	14
β-strand	378	1	16
α-helix	405-407	3
β-strand	410	1	15
β-strand	411-422	12	14
β-strand	427-431	5	14
β-strand	444-454	11	14
α-helix	459-462	4
α-helix	464-466	3
β-strand	468-471	4	14
α-helix	500-503	4
β-strand	507-510	4	17
β-strand	514-518	5	17
β-strand	530-531	2	17
α-helix	538-541	4
β-strand	575-576	2	17
β-strand	580-582	3	14
β-strand	592-593	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Selenocysteine-specific elongation factor	A, B	protein	616	Homo sapiens	P57772 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IZL_1 Selenocysteine-specific elongation factor (chains A, B)
MGSSHHHHHHSSGLVPRGSHMAGRRVNVNVGVLGHIDSGKTALARALSTTASTAAFDKQP
QSRERGITLDLGFSCFSVPLPARLRSSLPEFQAAPEAEPEPGEPLLQVTLVDCPGHASLI
RTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAI
DKMTKKMQKTLENTKFRGAPIIPVAAKPGGPEAPETEAPQGIPELIELLTSQISIPTRDP
SGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSA
MQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVG
HETVMGRLMFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSKDLTPAVTDNDEADKKAGQ
ATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGILLHGLEDRNYA
DSFLPRLKVYKLKHKHGLVERAMDDYSVIGRSLFKKETNIQLFVGLKVHLSTGELGIIDS
AFGQSGKFKIHIPGGLSPESKKILTPALKKRARAGRGEATRQEESAERSEPSQHVVLSLT
FKRYVFDTHKRMVQSP

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation. Dobosz-Bartoszek, M., Pinkerton, M.H., Otwinowski, Z. et al. Nat Commun (2016) 7:12941-12941. DOI 10.1038/ncomms12941 · PubMed

Other PDB entries of the same protein (UniProt P57772 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon
5IZK 3.25 Å, The crystal structure of human eEFSec in complex with GDP
5IZM 3.4 Å, The crystal structure of human eEFSec in complex with GDPNP

Browse structure collections

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