5J5O: Translation initiation factor 4E

Name: PDB 5J5O: Translation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog
Published: 2017-05-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Translation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog. Determined by X-ray diffraction at 1.87 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,401
Mol. weight: 91.24 kDa
Ligands: 6G0
Released: 10 May 2017

Explore 5J5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J5O contains 40 α-helices and 35 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: 9 helices, 9 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	69-76	8
β-strand	79	1	2
α-helix	82-84	3
β-strand	90-95	6	1
β-strand	111-116	6	1
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	162-167	6	1
α-helix	173-186	14
β-strand	196-199	4	1
α-helix	200-203	4
β-strand	215-216	2	1

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	38-48	11	3
β-strand	60-68	9	3
α-helix	69-76	8
β-strand	79	1	4
α-helix	82-84	3
α-helix	86	1
β-strand	90-95	6	3
β-strand	111-116	6	3
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	3
β-strand	162-167	6	3
α-helix	173-187	15
β-strand	196-199	4	3
α-helix	200-203	4
β-strand	215-216	2	3

Chain C: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	2
β-strand	38-48	11	5
α-helix	56-59	4
β-strand	60-68	9	5
α-helix	69-78	10
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	5
β-strand	111-116	6	5
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-156	8	5
β-strand	162-167	6	5
α-helix	173-187	15
β-strand	196-199	4	5
α-helix	200-202	3
β-strand	215-216	2	5

Chain D: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	4
α-helix	36-37	2
β-strand	38-48	11	6
α-helix	57-59	3
β-strand	60-68	9	6
α-helix	69-78	10
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	6
α-helix	105-108	4
β-strand	111-116	6	6
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-156	8	6
β-strand	162-167	6	6
α-helix	173-187	15
β-strand	198-199	2	6
α-helix	200-203	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A, B, C, D	protein	190	Mus musculus	P63073 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5J5O_1 Eukaryotic translation initiation factor 4E (chains A, B, C, D)
VANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMP
GCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSD
DVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKS
GSTTKNRFVV

Ligands and cofactors

ID	Name	Formula	Copies
6G0	5'-O-[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phospho…	C11 H20 N5 O17 P4	4

Water and common crystallization additives (GOL) are not listed.

Primary citation

mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation. Rydzik, A.M., Warminski, M., Sikorski, P.J. et al. Nucleic Acids Res (2017) 45:8661-8675. DOI 10.1093/nar/gkx569 · PubMed

Other PDB entries of the same protein (UniProt P63073 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M7X 1.68 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSepG mRNA 5' cap…
5M7Z 1.69 Å, Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap…
5M7V 1.74 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog…
5J5Y 1.75 Å, Translation initiation factor 4E in complex with m2(7,2'O)GppCCl2ppG mRNA 5' cap analog
6U09 1.79 Å, Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
1L8B 1.8 Å, Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to…
5M84 1.85 Å, Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog
6GKK 1.86 Å, Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide…
5M83 1.86 Å, Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpA mRNA 5' cap analog
5M81 1.9 Å, Translation initiation factor 4E in complex with (SP)-iPr-m7GppSpG mRNA 5' cap analog
5OSX 1.92 Å, Translation initiation factor 4E in complex with m7G(5'S)ppp(5'S)G mRNA 5' cap analog
6U06 1.96 Å, Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking

Browse structure collections

About this viewer

MolViewer shows 5J5O directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.