5IZK: Human eEFSec

The crystal structure of human eEFSec in complex with GDP. Determined by X-ray diffraction at 3.25 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,060
Mol. weight: 136.01 kDa
Ligands: GDP
Released: 12 Oct 2016

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

Secondary structure: helices and β-sheets

5IZK contains 18 α-helices and 75 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: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	20-29	10
β-strand	54	1	1
β-strand	57	1	1
β-strand	86-91	6	1
α-helix	97-104	8
α-helix	107-109	3
β-strand	110-118	9	1
α-helix	126-137	12
β-strand	141-146	6	1
α-helix	153-171	19
β-strand	181-183	3	1
α-helix	202-212	11
β-strand	225-230	6	2
β-strand	242-247	6	2
β-strand	255-257	3	2
β-strand	264-271	8	2
β-strand	287-290	4	2
β-strand	302-304	3	2
β-strand	310-319	10	3
β-strand	321	1	4
β-strand	330	1	5
β-strand	337-338	2	6
β-strand	343-344	2	6
β-strand	346-347	2	3
β-strand	350-352	3	3
α-helix	360-362	3
β-strand	373-376	4	3
β-strand	378	1	5
β-strand	410-422	13	3
β-strand	427-428	2	3
β-strand	429-430	2	6
β-strand	446	1	4
β-strand	448-454	7	3
β-strand	469-470	2	3
β-strand	473-478	6	7
β-strand	479	1	8
β-strand	484	1	9
β-strand	487	1	9
β-strand	488	1	10
β-strand	490	1	8
β-strand	507-510	4	7
β-strand	515-517	3	7
β-strand	518	1	10
β-strand	530	1	10
α-helix	538-542	5
β-strand	574-579	6	7
β-strand	582	1	3

Chain B: 10 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	11
α-helix	21-29	9
β-strand	87-91	5	11
α-helix	96-105	10
α-helix	106-109	4
β-strand	112-118	7	11
α-helix	125-137	13
β-strand	141-146	6	11
α-helix	155-170	16
β-strand	181-183	3	11
α-helix	204-209	6
α-helix	210-212	3
β-strand	225-227	3	12
β-strand	242-247	6	12
β-strand	255-258	4	12
β-strand	263-271	9	12
β-strand	285-290	6	12
β-strand	302-304	3	12
β-strand	310-311	2	13
β-strand	314-319	6	14
β-strand	321	1	15
β-strand	330	1	16
β-strand	336-338	3	15
β-strand	343-345	3	15
β-strand	349-351	3	14
β-strand	352	1	17
α-helix	357-359	3
β-strand	372-374	3	17
β-strand	378	1	16
β-strand	410-415	6	14
β-strand	421-422	2	13
β-strand	428-430	3	15
β-strand	446-448	3	15
β-strand	450-453	4	14
α-helix	464-466	3
β-strand	468-470	3	17
β-strand	474-479	6	18
β-strand	487-488	2	18
β-strand	490-491	2	18
β-strand	507-510	4	18
β-strand	515-518	4	18
β-strand	530-531	2	18
α-helix	541-543	3
β-strand	574-578	5	18
β-strand	582	1	17

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

>5IZK_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
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	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:

5IZL 2.72 Å, The crystal structure of human eEFSec in complex with GDPCP
7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon
5IZM 3.4 Å, The crystal structure of human eEFSec in complex with GDPNP

Browse structure collections

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