5NVM: PDB entry 5NVM

Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,536
Mol. weight: 54.38 kDa
Ligands: PO4
Released: 26 Jul 2017

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

Secondary structure: helices and β-sheets

5NVM contains 18 α-helices and 18 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-68	14	1
α-helix	77-78	2
β-strand	79-90	12	1
α-helix	91-98	8
β-strand	101	1	2
α-helix	104-106	3
β-strand	110-117	8	1
β-strand	133-139	7	1
α-helix	144-156	13
β-strand	166-173	8	1
β-strand	178-184	7	1
α-helix	190-204	15
β-strand	213-216	4	1
α-helix	217-220	4

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-50	6
α-helix	60-62	3
α-helix	65-70	6
β-strand	71	1	2

Chain C: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-66	12	3
β-strand	82-90	9	3
α-helix	91-99	9
β-strand	101	1	4
α-helix	102-103	2
α-helix	104-106	3
β-strand	111-117	7	3
β-strand	133-140	8	3
α-helix	144-156	13
β-strand	166-173	8	3
β-strand	177-184	8	3
α-helix	190-203	14
β-strand	212-216	5	3

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-50	6
α-helix	58-59	2
α-helix	60-62	3
α-helix	65-70	6
β-strand	71	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E type 2	A, C	protein	189	Homo sapiens	O60573 (AlphaFold model)
GRB10-interacting GYF protein 2	B, D	protein	42	Homo sapiens	Q6Y7W6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5NVM_1 Eukaryotic translation initiation factor 4E type 2 (chains A, C)
GPHMLEAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPG
DLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEE
ICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTHTDSIKMPG
RLGPQRLLF

Sequence of entity 2 (B, D), FASTA

>5NVM_2 GRB10-interacting GYF protein 2 (chains B, D)
GPHMKYKLADYRYGREEMLALFLKDNKIPSDLLDKEFLPILQ

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

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
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
5NVK 2.9 Å, Crystal structure of the human 4EHP-GIGYF1 complex

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