5IZM: Human eEFSec

The crystal structure of human eEFSec in complex with GDPNP. Determined by X-ray diffraction at 3.4 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,632
Mol. weight: 137.88 kDa
Ligands: GNP, MN
Released: 12 Oct 2016

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

Secondary structure: helices and β-sheets

5IZM contains 24 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: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	1
α-helix	20-29	10
β-strand	52-59	8	1
α-helix	60-61	2
α-helix	62-65	4
β-strand	85-92	8	1
α-helix	97-99	3
α-helix	100-106	7
β-strand	112-118	7	1
α-helix	125-137	13
β-strand	140-146	7	1
α-helix	156-172	17
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	250-251	2	4
β-strand	255	1	5
β-strand	257	1	3
β-strand	266	1	5
β-strand	271	1	6
β-strand	276	1	6
β-strand	279-280	2	4
β-strand	285-286	2	3
β-strand	289-290	2	3
β-strand	301-304	4	3
β-strand	312-318	7	7
β-strand	320-321	2	7
α-helix	322	1
β-strand	330	1	8
β-strand	335-340	6	7
β-strand	342-347	6	7
β-strand	350-353	4	7
β-strand	373-375	3	7
β-strand	378	1	8
β-strand	411-420	10	7
β-strand	427	1	9
β-strand	429-431	3	7
β-strand	444-447	4	7
β-strand	449	1	9
β-strand	452-454	3	7
α-helix	459-462	4
α-helix	464-466	3
β-strand	469-470	2	7
β-strand	487	1	10
β-strand	507	1	11
β-strand	510	1	12
β-strand	514	1	12
β-strand	517	1	11
β-strand	531	1	10
β-strand	582	1	7

Chain B: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	11-14	4	13
α-helix	20-30	11
β-strand	52-59	8	13
α-helix	60-61	2
α-helix	62-64	3
β-strand	85-92	8	13
α-helix	97-99	3
α-helix	100-105	6
β-strand	112-118	7	13
α-helix	125-137	13
β-strand	140-146	7	13
α-helix	157-170	14
β-strand	181-183	3	13
α-helix	203-212	10
β-strand	225-232	8	14
β-strand	239-247	9	14
β-strand	249-251	3	15
β-strand	255-258	4	14
β-strand	263-266	4	14
β-strand	269-272	4	14
β-strand	275-276	2	14
β-strand	279-281	3	15
β-strand	285	1	14
β-strand	287-290	4	14
α-helix	295-297	3
β-strand	302-304	3	14
β-strand	310-321	12	16
β-strand	334-339	6	16
β-strand	342-353	12	16
β-strand	373-375	3	16
β-strand	411-422	12	16
β-strand	427-430	4	16
β-strand	446-454	9	16
α-helix	459-462	4
α-helix	464-466	3
β-strand	469-471	3	16
β-strand	474-476	3	17
β-strand	478-479	2	18
β-strand	487	1	17
β-strand	490-491	2	18
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	538-543	6
β-strand	575-578	4	17
β-strand	581-582	2	16

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

>5IZM_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
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
MN	Manganese (II) ion	Mn	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
5IZK 3.25 Å, The crystal structure of human eEFSec in complex with GDP

Browse structure collections

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