8PHD: Human Cdc123

Structure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP. Determined by X-ray diffraction at 2.08 Å resolution. Released 16 Aug 2023.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,874
Mol. weight: 108.46 kDa
Ligands: MG, ATP
Released: 16 Aug 2023

Explore 8PHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PHD contains 43 α-helices and 43 β-strands across 4 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	11-14	4
α-helix	15-17	3
α-helix	19-21	3
β-strand	22	1	1
β-strand	25-29	5	2
α-helix	30-31	2
α-helix	32-38	7
β-strand	44	1	3
β-strand	77	1	4
α-helix	84-96	13
β-strand	101-104	4	2
α-helix	111-116	6
α-helix	118-120	3
β-strand	124	1	2
α-helix	127-134	8
α-helix	138-145	8
α-helix	155-160	6
β-strand	163-168	6	2
α-helix	172-173	2
β-strand	177-183	7	1
β-strand	186-192	7	1
α-helix	200-204	5
α-helix	206-216	11
α-helix	217-221	5
β-strand	230-236	7	1
β-strand	242-249	8	1
α-helix	261-266	6
α-helix	285	1
β-strand	286-288	3	1
α-helix	319-335	17

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	366-377	12	3
β-strand	380	1	5
α-helix	392-393	2
β-strand	394	1	5
α-helix	395-398	4
β-strand	400	1	4
β-strand	403-408	6	3
β-strand	411-420	10	3
β-strand	424-435	12	3
β-strand	440-446	7	3
β-strand	451-464	14	3

Chain C: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	11-14	4
α-helix	15-17	3
α-helix	19-21	3
β-strand	22	1	6
β-strand	25-29	5	7
α-helix	30-31	2
α-helix	32-38	7
β-strand	44	1	8
β-strand	77	1	9
α-helix	84-96	13
β-strand	101-104	4	7
α-helix	111-116	6
α-helix	118-120	3
β-strand	124	1	7
α-helix	127-134	8
α-helix	138-144	7
α-helix	156-159	4
β-strand	163-168	6	7
α-helix	172-173	2
β-strand	177-183	7	6
β-strand	186-192	7	6
α-helix	200-204	5
α-helix	206-216	11
α-helix	217-221	5
β-strand	230-236	7	6
β-strand	242-248	7	6
α-helix	261-265	5
α-helix	285	1
β-strand	286-288	3	6
α-helix	302-305	4
α-helix	320-331	12

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	366-374	9	8
β-strand	376-377	2	8
β-strand	380	1	10
α-helix	392-393	2
β-strand	394	1	10
α-helix	396-398	3
β-strand	400	1	9
β-strand	403-408	6	8
β-strand	411-420	10	8
β-strand	424-435	12	8
β-strand	440-446	7	8
β-strand	451-464	14	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division cycle protein 123 homolog	A, C	protein	356	Homo sapiens	O75794 (AlphaFold model)
Eukaryotic translation initiation factor 2 subunit 3	B, D	protein	111	Homo sapiens	P41091 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8PHD_1 Cell division cycle protein 123 homolog (chains A, C)
MGSSHHHHHHSSGLVPRGSHMKKEHVLHCQFSAWYPFFRGVTIKSVILPLPQNVKDYLLD
DGTLVVSGRDDPPTHSQPDSDDEAEEIQWSDDENTATLTAPEFPEFATKVQEAINSLGGS
VFPKLNWSAPRDAYWIAMNSSLKCKTLSDIFLLFKSSDFITRDFTQPFIHCTDDSPDPCI
EYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEIRRCIQDFFKKH
IQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELISENNLNGDFSEVDAQ
EQDSPAFRCTNSEVTVQPSPYLSYRLPKDFVDLSTGEDAHKLIDFLKLKRNQQEDD

Sequence of entity 2 (B, D), FASTA

>8PHD_2 Eukaryotic translation initiation factor 2 subunit 3 (chains B, D)
MALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVK
ADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD

Ligands and cofactors

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

Primary citation

Binding of human Cdc123 to eIF2 gamma. Cardenal Peralta, C., Vandroux, P., Neumann-Arnold, L. et al. J Struct Biol (2023) 215:108006-108006. DOI 10.1016/j.jsb.2023.108006 · PubMed

Other PDB entries of the same protein (UniProt O75794 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PHV 1.97 Å, Structure of Human selenomethionylated Cdc123 bound to domain 3 of eIF2 gamma

Browse structure collections

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