6GKL: Translation initiation factor 4E

Name: PDB 6GKL: Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2)
Published: 2019-06-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2). Determined by X-ray diffraction at 2.2 Å resolution. Released 19 Jun 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,908
Mol. weight: 93.31 kDa
Ligands: G0Z
Released: 19 Jun 2019

Explore 6GKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GKL contains 40 α-helices and 36 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	38-49	12	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
α-helix	86	1
β-strand	89-95	7	1
β-strand	111-117	7	1
α-helix	119-121	3
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-156	8	1
β-strand	161-167	7	1
α-helix	173-187	15
β-strand	196-199	4	1
α-helix	200-204	5
β-strand	215-216	2	1

Chain B: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	38-49	12	3
α-helix	57-59	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	89-95	7	3
β-strand	111-117	7	3
α-helix	119-121	3
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-156	8	3
β-strand	161-167	7	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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	4
β-strand	38-49	12	5
α-helix	57-59	3
β-strand	60-68	9	5
α-helix	69-76	8
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	5
β-strand	111-117	7	5
α-helix	119-124	6
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-156	8	5
β-strand	161-167	7	5
α-helix	173-187	15
β-strand	196-199	4	5
α-helix	200-203	4
β-strand	215-216	2	5

Chain D: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	2
β-strand	38-48	11	6
α-helix	57-59	3
β-strand	60-68	9	6
α-helix	69-76	8
α-helix	82-84	3
α-helix	86	1
β-strand	89-95	7	6
β-strand	111-116	6	6
α-helix	119-121	3
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	196-199	4	6
α-helix	200-203	4
β-strand	215-216	2	6

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

>6GKL_1 Eukaryotic translation initiation factor 4E (chains A, B, C, D)
VANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMP
GCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSD
DVCGAVVNVRAKGDKIAIWTTECENRDAVTHIGRVYKERLGLPPKIVIGYQSHADTATKS
GSTTKNRFVV

Ligands and cofactors

ID	Name	Formula	Copies
G0Z	[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R}…	C31 H45 N15 O22 P4 S	4

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

Primary citation

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2). Warminski, M., Nowak, E., Kubacka, D. et al. To be published.

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
5J5O 1.87 Å, Translation initiation factor 4E in complex with m7GppppG 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

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