8B9X: PDB entry 8B9X

Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1. Determined by X-ray diffraction at 3.07 Å resolution. Released 25 Oct 2023.

Method: X-ray diffraction
Resolution: 3.07 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,076
Mol. weight: 61.82 kDa
Released: 25 Oct 2023

Explore 8B9X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B9X contains 27 α-helices and 28 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: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-19	18
β-strand	22-24	3	1
α-helix	25-31	7
α-helix	36-49	14
β-strand	54-56	3	1
β-strand	61-64	4	1
α-helix	67-80	14
β-strand	82-84	3	2
α-helix	85-96	12
α-helix	102-114	13
β-strand	121-122	2	2
β-strand	128-130	3	2
α-helix	132-145	14
β-strand	149-151	3	3
α-helix	152-159	8
α-helix	164-167	4
α-helix	170-176	7
β-strand	180-183	4	3
β-strand	186-189	4	3
α-helix	190-207	18
β-strand	209-211	3	4
α-helix	212-219	8
α-helix	223-231	9
β-strand	234	1	5
β-strand	238	1	5
β-strand	240-244	5	4
β-strand	248-252	5	4

Chain B: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-5	5
α-helix	6-19	14
β-strand	22-24	3	6
α-helix	25-31	7
α-helix	36-49	14
β-strand	54-56	3	6
β-strand	61-64	4	6
α-helix	67-80	14
β-strand	82-84	3	7
α-helix	85-96	12
α-helix	102-114	13
β-strand	121-122	2	7
β-strand	128-130	3	7
α-helix	132-145	14
β-strand	149-151	3	8
α-helix	152-159	8
α-helix	164-167	4
α-helix	170-176	7
β-strand	180-183	4	8
β-strand	186-189	4	8
α-helix	190-207	18
β-strand	209-211	3	9
α-helix	212-219	8
α-helix	223-231	9
β-strand	234	1	10
β-strand	238	1	10
β-strand	240-244	5	9
β-strand	248-252	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1	A, B	protein	274	Homo sapiens	O94874 (AlphaFold model), Q96HY6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8B9X_1 DDRGK domain-containing protein 1,E3 UFM1-protein ligase 1 (chains A, B)
GMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDR
GKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGLSERNCIEIVNKLIAQKQLE
VVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKH
VQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIIS
GHIDLDNRGVIFTEAFVARHKARIRGLFSAITRP

Primary citation

Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation. Banerjee, S., Varga, J.K., Kumar, M. et al. EMBO Rep (2023) 24:e56920-e56920. DOI 10.15252/embr.202356920 · PubMed

Other PDB entries of the same protein (UniProt O94874 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QFD 2.2 Å, UFL1 E3 ligase bound 60S ribosome
8C0D 2.56 Å, UFL1/DDRGK1 bound to UFC1
8OJ5 2.9 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)
9GY4 3.0 Å, 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF…
8OHD 3.1 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)
8QFC 3.2 Å, UFL1 E3 ligase bound 60S ribosome
8OJ0 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)
8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)

Browse structure collections

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