7XTP: EIF4E

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain. Determined by X-ray diffraction at 1.83 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,357
Mol. weight: 84.34 kDa
Ligands: MGO
Released: 27 Jul 2022

Explore 7XTP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XTP contains 34 α-helices and 37 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	38-48	11	1
α-helix	57-59	3
β-strand	60-68	9	1
α-helix	69-78	10
α-helix	80-81	2
α-helix	82-84	3
α-helix	86	1
β-strand	90-95	6	1
β-strand	111-116	6	1
α-helix	121-124	4
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	162-167	6	1
α-helix	173-187	15
β-strand	195-199	5	1
α-helix	200-203	4

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	38-48	11	2
α-helix	57-59	3
β-strand	60-68	9	2
α-helix	69-78	10
α-helix	80-81	2
α-helix	82-84	3
α-helix	86	1
β-strand	90-95	6	2
β-strand	111-116	6	2
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	2
β-strand	162-167	6	2
α-helix	173-187	15
β-strand	194-199	6	2
α-helix	200-204	5

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
β-strand	11-13	3	4
β-strand	19-26	8	3
α-helix	30-32	3
β-strand	35-40	6	4
β-strand	47-53	7	4
β-strand	58-61	4	4
β-strand	69-74	6	3
α-helix	75-77	3
β-strand	79-84	6	3
α-helix	89-91	3
β-strand	93-100	8	4
α-helix	102-104	3
α-helix	109-116	8
α-helix	117-120	4
β-strand	121-124	4	4
β-strand	128-132	5	4

Chain D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	5
β-strand	12-13	2	6
β-strand	19-26	8	5
α-helix	30-32	3
β-strand	35-40	6	7
β-strand	47-53	7	7
β-strand	58-61	4	7
α-helix	63-65	3
β-strand	69-74	6	5
α-helix	75-77	3
β-strand	79-84	6	5
α-helix	89-91	3
β-strand	93-100	8	7
α-helix	102-104	3
α-helix	109-116	8
α-helix	117-120	4
β-strand	121-124	4	7
β-strand	128-130	3	7
β-strand	131-132	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A, B	protein	217	Homo sapiens	P06730 (AlphaFold model)
VH-S4ss	C, D	protein	154	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7XTP_1 Eukaryotic translation initiation factor 4E (chains A, B)
MATVEPETTPTPNPPTTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANL
RLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQ
QRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIG
RVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Sequence of entity 2 (C, D), FASTA

>7XTP_2 VH-S4ss (chains C, D)
MSEVQLVESGGGLVQPGGSLRLSCAISGFSISSTSIDWVRQAPGKGLEWVARISPSSGST
SYADSVKGRFTISADTSKNTVYLQMNSLRAEDTAVYYCGRVAKALNSRSPSFVVNTYSSI
GFDYRGQGTLVTVSSGAAEQKLISEEDLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MGO	[[(2R,3S,4R,5R)-5-(6-amino-3-methyl-4-oxo-5H-IMIDAZO[4,5-c]pyridin-1-yl)-3,4-di…	C12 H20 N4 O14 P3	2

Primary citation

Engineering an autonomous VH domain to modulate intracellular pathways and to interrogate the eIF4F complex. Frosi, Y., Lin, Y.C., Shimin, J. et al. Nat Commun (2022) 13:4854-4854. DOI 10.1038/s41467-022-32463-1 · PubMed

Other PDB entries of the same protein (UniProt P06730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TPW 1.5 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5T46 1.53 Å, Crystal structure of the human eIF4E-eIF4G complex
8QM8 1.58 Å, Potential drug binding sites for translation initiation factor eIF4E
4TQB 1.59 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZJY 1.59 Å, Stapled-peptides tailored against initiation of translation
7D6Y 1.67 Å, eIF4E in Complex with a Disulphide-Free Autonomous VH Domain
5ZJZ 1.67 Å, Stapled-peptides tailored against initiation of translation
5EI3 1.71 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
4UED 1.75 Å, Complex of human eIF4E with the 4E binding protein 4E-BP1
5ZK9 1.76 Å, Stapled-peptides tailored against initiation of translation
4TQC 1.8 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZML 1.8 Å, Stapled-peptides tailored against initiation of translation

Browse structure collections

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