5NVK: Human 4EHP-GIGYF1 complex

Crystal structure of the human 4EHP-GIGYF1 complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,833
Mol. weight: 122.85 kDa
Released: 26 Jul 2017

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

Secondary structure: helices and β-sheets

5NVK contains 54 α-helices and 44 β-strands across 8 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	53	1	1
β-strand	55-66	12	2
β-strand	83-90	8	2
α-helix	91-98	8
β-strand	101	1	3
α-helix	104-106	3
β-strand	111-117	7	2
β-strand	133-139	7	2
α-helix	144-156	13
β-strand	166-173	8	2
β-strand	178-184	7	2
α-helix	190-204	15
α-helix	206-207	2
β-strand	213-216	4	2
α-helix	217-220	4

Chains B and H: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-48	6
α-helix	55-57	3
α-helix	58-61	4
α-helix	63-65	3
β-strand	69	1	3
α-helix	77-79	3
α-helix	81-83	3
α-helix	84-92	9
β-strand	95	1	2
α-helix	97-100	4

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-66	12	4
β-strand	83-90	8	4
α-helix	91-98	8
β-strand	101	1	5
α-helix	104-106	3
β-strand	111-117	7	4
β-strand	133-139	7	4
α-helix	144-156	13
β-strand	166-173	8	4
β-strand	178-184	7	4
α-helix	190-203	14
β-strand	213-216	4	4

Chain D: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	1
α-helix	43-48	6
α-helix	59-61	3
α-helix	63-65	3
β-strand	69	1	5
α-helix	73-76	4
α-helix	77-79	3
α-helix	84-89	6
β-strand	95	1	4
α-helix	97-100	4

Chain E: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-66	12	6
α-helix	67-69	3
α-helix	75-80	6
β-strand	83-90	8	6
α-helix	91-98	8
β-strand	101	1	7
α-helix	102-103	2
α-helix	104-106	3
β-strand	111-117	7	6
α-helix	127-130	4
β-strand	133-139	7	6
α-helix	144-156	13
β-strand	166-173	8	6
β-strand	178-184	7	6
α-helix	190-204	15
β-strand	213-216	4	6

Chain F: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	43-48	6
α-helix	55-57	3
α-helix	58-61	4
α-helix	63-65	3
β-strand	69	1	7
α-helix	77-79	3
α-helix	84-90	7
β-strand	95	1	6
α-helix	97-100	4

Chain G: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	55-66	12	8
β-strand	82-90	9	8
α-helix	91-98	8
β-strand	101	1	9
α-helix	104-106	3
β-strand	111-117	7	8
β-strand	133-139	7	8
α-helix	144-156	13
β-strand	166-173	8	8
β-strand	178-184	7	8
α-helix	190-204	15
α-helix	206-207	2
β-strand	213-216	4	8
α-helix	217-220	4
β-strand	223	1	10
β-strand	226	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E type 2	A, C, E, G	protein	189	Homo sapiens	O60573 (AlphaFold model)
GRB10-interacting GYF protein 1	B, D, F, H	protein	75	Homo sapiens	O75420 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5NVK_1 Eukaryotic translation initiation factor 4E type 2 (chains A, C, E, G)
GPHMLEAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPG
DLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEE
ICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTHTDSIKMPG
RLGPQRLLF

Sequence of entity 2 (B, D, F, H), FASTA

>5NVK_2 GRB10-interacting GYF protein 1 (chains B, D, F, H)
GPHMKYKLADYRYGREEMLALYVKENKVPEELQDKEFAAVLQDEPLQPLALEPLTEEEQR
NFSLSVNSVAVLRLM

Primary citation

GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression. Peter, D., Weber, R., Sandmeir, F. et al. Genes Dev (2017) 31:1147-1161. DOI 10.1101/gad.299420.117 · PubMed

Other PDB entries of the same protein (UniProt O60573 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2JGB 1.7 Å, Structure of human eIF4E homologous protein 4EHP with m7GTP
5NVN 1.9 Å, Crystal structure of the human 4EHP-4E-BP1 complex
5XLN 1.9 Å, Crystal structure of the TRS_UNE-T and 4EHP complex
5NVM 2.0 Å, Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences
5NVL 2.3 Å, Crystal structure of the human 4EHP-GIGYF2 complex
2JGC 2.4 Å, Structure of the human eIF4E homologous protein, 4EHP without ligand bound

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