3M63: Ufd2

Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2. Determined by X-ray diffraction at 2.4 Å resolution. Released 28 Apr 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 8,488
Mol. weight: 122.62 kDa
Released: 28 Apr 2010

Explore 3M63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M63 contains 66 α-helices and 18 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: 64 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	-3-8	12
β-strand	10-11	2	1
α-helix	20	1
β-strand	21-22	2	1
α-helix	23	1
α-helix	28-30	3
α-helix	39-44	6
α-helix	45-49	5
α-helix	56-75	20
α-helix	80-83	4
α-helix	84-101	18
α-helix	113-122	10
α-helix	124-126	3
α-helix	128-140	13
α-helix	144-161	18
α-helix	171-186	16
α-helix	188-191	4
α-helix	194-196	3
α-helix	202-203	2
α-helix	208-210	3
α-helix	211-214	4
α-helix	218-221	4
α-helix	228-231	4
α-helix	232-236	5
α-helix	243-274	32
α-helix	276-291	16
α-helix	294-297	4
α-helix	303-305	3
α-helix	309-323	15
α-helix	324-327	4
α-helix	334-336	3
β-strand	356	1	2
α-helix	361-371	11
α-helix	381-392	12
α-helix	393-397	5
α-helix	398-405	8
α-helix	407-421	15
α-helix	429-460	32
α-helix	463-484	22
α-helix	494-496	3
α-helix	501-503	3
α-helix	512-517	6
α-helix	523-525	3
β-strand	527	1	2
α-helix	529-541	13
α-helix	555-567	13
α-helix	575-587	13
α-helix	591-592	2
α-helix	596-598	3
α-helix	601-606	6
α-helix	608-611	4
α-helix	614-624	11
α-helix	637-654	18
α-helix	656-668	13
α-helix	670-706	37
α-helix	720-754	35
α-helix	756-759	4
α-helix	762-780	19
α-helix	782-785	4
α-helix	792-795	4
α-helix	799-812	14
α-helix	817-825	9
α-helix	832-842	11
α-helix	851-878	28
α-helix	883-885	3
β-strand	886	1	3
β-strand	893	1	3
β-strand	897-899	3	4
β-strand	906-908	3	4
α-helix	909-916	8
β-strand	921	1	5
β-strand	928	1	5
α-helix	931-933	3
β-strand	935-936	2	4
α-helix	938-953	16

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	16	1	6
β-strand	23	1	7
α-helix	24-35	12
β-strand	44-46	3	6
β-strand	49-50	2	6
β-strand	56	1	7
α-helix	62-63	2
β-strand	66-70	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin conjugation factor E4	A	protein	968	Saccharomyces cerevisiae	P54860 (AlphaFold model)
Ubiquitin domain-containing protein DSK2	B	protein	101	Saccharomyces cerevisiae	P48510 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3M63_1 Ubiquitin conjugation factor E4 (chains A)
GSPEFRSMTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFIDTLLLYQLTENEKL
DKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGVVALQIENFCMNGAF
INYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYCNKHVSHFDLNESVI
YNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGPILSLSPIEAAVAIR
NYGDNLLRSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSRTDMISYFAHIANKN
HLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDANYFNNPSLFIDLSG
ETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGGTLSFEEKMGSEIKA
LKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGFFAHRSLQLEVFDFI
CGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHAPVPFKYYPEFVVEG
PVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKGKLVQLLSVGAMPLT
DNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFNSRYSISIILEELYY
KIPSYKNQLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVHNIQNELDNRARGAP
PTREEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAFVTPEIVYRLASMLN
YNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEFISAVAKDERSFNRN
LFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYGDVPDEFLDPLMYTI
MKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCFKKQKKE
EAKHKASE

Sequence of entity 2 (B), FASTA

>3M63_2 Ubiquitin domain-containing protein DSK2 (chains B)
MKHHHHHHPMSDYDIPTTENLYFQGAMSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKA
NGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP

Primary citation

The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. Hanzelmann, P., Stingele, J., Hofmann, K. et al. J Biol Chem (2010) 285:20390-20398. DOI 10.1074/jbc.M110.112532 · PubMed

Other PDB entries of the same protein (UniProt P54860 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3M62 2.4 Å, Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23
2QIZ 2.56 Å, Structure of the yeast U-box-containing ubiquitin ligase Ufd2p
2QJ0 2.65 Å, Structure of the yeast U-box-containing ubiquitin ligase Ufd2p
9M7O 4.14 Å, Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)
9KHS 4.31 Å, Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)
9KHT 4.85 Å, cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)

Browse structure collections

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