3FN1: NEDD8-activating enzyme E1 catalytic subunit

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Mar 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,127
Mol. weight: 29.96 kDa
Released: 17 Mar 2009

Explore 3FN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FN1 contains 11 α-helices and 17 β-strands across 2 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	351-355	5	1
β-strand	360	1	2
α-helix	361-370	10
β-strand	380-385	6	1
β-strand	388-394	7	1
α-helix	398-404	7
α-helix	405-409	5
β-strand	411	1	2
α-helix	417-418	2
β-strand	422-426	5	1
β-strand	434-440	7	1

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	32-44	13
α-helix	45-47	3
β-strand	52-55	4	3
β-strand	64-69	6	3
β-strand	81-86	6	3
β-strand	91	1	4
β-strand	94	1	4
α-helix	95-96	2
β-strand	97-100	4	3
β-strand	109	1	5
β-strand	115	1	5
α-helix	118-120	3
β-strand	122	1	6
β-strand	130	1	6
α-helix	136-145	10
α-helix	159-167	9
α-helix	169-183	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8-activating enzyme E1 catalytic subunit	A	protein	98	Homo sapiens	Q8TBC4 (AlphaFold model)
NEDD8-conjugating enzyme UBE2F	B	protein	167	Homo sapiens	Q969M7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FN1_1 NEDD8-activating enzyme E1 catalytic subunit (chains A)
GSSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERT
RPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS

Sequence of entity 2 (B), FASTA

>3FN1_2 NEDD8-conjugating enzyme UBE2F (chains B)
GSATASDSTRRVSVRDKLLVKEVAELEANLPCTCKVHFPDPNKLHCFQLTVTPDEGYYQG
GKFQFETEVPDAYNMVPPKVKCLTKIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKD
VVWGLNSLFTDLLNFDDPLNIEAAEHHLRDKEDFRNKVDDYIKRYAR

Primary citation

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification. Huang, D.T., Ayrault, O., Hunt, H.W. et al. Mol Cell (2009) 33:483-495. DOI 10.1016/j.molcel.2009.01.011 · PubMed

Other PDB entries of the same protein (UniProt Q8TBC4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JJM 2.15 Å, Crystal Structure of Homodimeric Androgen Receptor Ligand-Binding Domain bound to DHT…
1Y8X 2.4 Å, Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1
1TT5 2.6 Å, Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal…
1YOV 2.6 Å, Insights into the Ubiquitin Transfer Cascade from the refined structure of the…
3DBH 2.85 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
3DBL 2.9 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
1R4M 3.0 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex
3GZN 3.0 Å, Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924
3DBR 3.05 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
1R4N 3.6 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP
2LQ7 E2 binding surface on Uba3 beta-grasp domain undergoes a conformational transition

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