2RG8: Programmed for Cell Death 4 Middle MA3 domain

Crystal Structure of Programmed for Cell Death 4 Middle MA3 domain. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Mar 2008.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,705
Mol. weight: 36.14 kDa
Released: 4 Mar 2008

Explore 2RG8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RG8 contains 18 α-helices and 4 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: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	161-178	18
α-helix	181-191	11
α-helix	195-198	4
α-helix	199-209	11
α-helix	213-226	14
β-strand	227	1	1
β-strand	231	1	1
α-helix	233-253	21
α-helix	257-270	14
α-helix	278-281	4
α-helix	289-303	15

Chain B: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	161-178	18
α-helix	181-191	11
α-helix	194-198	5
α-helix	199-209	11
α-helix	213-226	14
β-strand	227	1	2
β-strand	231	1	2
α-helix	233-253	21
α-helix	257-270	14
α-helix	278-281	4
α-helix	289-304	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death protein 4	A, B	protein	165	Homo sapiens	Q53EL6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2RG8_1 Programmed cell death protein 4 (chains A, B)
GLPLDERAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASH
REMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILC
NTYIDSYKGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGG

Primary citation

PDCD4 inhibits translation initiation by binding to eIF4A using both its MA3 domains. Suzuki, C., Garces, R.G., Edmonds, K.A. et al. Proc Natl Acad Sci U S A (2008) 105:3274-3279. DOI 10.1073/pnas.0712235105 · PubMed

Other PDB entries of the same protein (UniProt Q53EL6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9TES 1.22 Å, Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
9BKD 2.6 Å, The structure of human Pdcd4 bound to the 40S small ribosomal subunit
2ZU6 2.8 Å, crystal structure of the eIF4A-PDCD4 complex
3EIJ 2.8 Å, Crystal structure of Pdcd4
8XXL 2.9 Å, Cryo-EM structure of the human 40S ribosome with PDCD4
8XXM 3.2 Å, Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G
8XXN 3.6 Å, Cryo-EM structure of the human 43S ribosome with PDCD4
9BLN 3.9 Å, The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex
2GGF Solution structure of the MA3 domain of human Programmed cell death 4
2KZT Structure of the Tandem MA-3 Region of Pdcd4

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