4NRG: Human Mms2/Ubc13 D118G mutant

Crystal Structure of a human Mms2/Ubc13 D118G mutant. Determined by X-ray diffraction at 1.95 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,500
Mol. weight: 35.05 kDa
Released: 10 Dec 2014

Explore 4NRG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NRG contains 17 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	11-24	14
β-strand	31-35	5	1
β-strand	45-51	7	1
α-helix	52-53	2
β-strand	62-68	7	1
α-helix	77-78	2
β-strand	79-82	4	1
β-strand	84	1	2
β-strand	91	1	3
β-strand	97	1	1
β-strand	98	1	3
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	129-132	4
α-helix	134-138	5
β-strand	142	1	2

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	4
β-strand	34-40	7	4
α-helix	41-42	2
β-strand	51-57	7	4
α-helix	66-67	2
β-strand	68-71	4	4
β-strand	77	1	5
β-strand	80	1	5
β-strand	85	1	4
β-strand	86	1	5
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 variant 2	A	protein	153	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	160	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NRG_1 Ubiquitin-conjugating enzyme E2 variant 2 (chains A)
GPLGSPEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIG
PPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNS
YSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 2 (B), FASTA

>4NRG_2 Ubiquitin-conjugating enzyme E2 N (chains B)
GPLGSPEFMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTF
KLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALL
SAPNPGDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Primary citation

Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes. Rout, M.K., Hodge, C.D., Markin, C.J. et al. J Am Chem Soc (2014) 136:17446-17458. DOI 10.1021/ja505440b · PubMed

Other PDB entries of the same protein (UniProt Q15819 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
9LHJ 1.68 Å, UBE2N/UBE2V2 complexed with a covalent inhibitor
8WR5 1.7 Å, The Crystal Structure of Mms2 from Biortus
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
1J74 1.9 Å, Crystal Structure of Mms2
9N1F 2.1 Å, Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex
7BBD 2.2 Å, Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin…
4NRI 2.3 Å, Crystal Structure of a human Mms2/Ubc13 A122G mutant

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