2QIZ: Yeast U-box-containing ubiquitin ligase Ufd2p

Name: PDB 2QIZ: Structure of the yeast U-box-containing ubiquitin ligase Ufd2p
Published: 2007-09-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of the yeast U-box-containing ubiquitin ligase Ufd2p. Determined by X-ray diffraction at 2.56 Å resolution. Released 18 Sept 2007.

Method: X-ray diffraction
Resolution: 2.56 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 7,767
Mol. weight: 112.27 kDa
Released: 18 Sept 2007

Explore 2QIZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QIZ contains 62 α-helices and 11 β-strands across 1 chain. 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: 62 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	-2-8	11
β-strand	10-11	2	1
β-strand	21-22	2	1
α-helix	36-38	3
α-helix	39-48	10
α-helix	56-74	19
α-helix	81-101	21
α-helix	113-122	10
α-helix	124-126	3
α-helix	128-140	13
α-helix	144-161	18
α-helix	171-185	15
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
α-helix	354-355	2
β-strand	356	1	2
α-helix	361-370	10
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	501-502	2
α-helix	511-517	7
α-helix	523-525	3
β-strand	527	1	2
α-helix	529-541	13
α-helix	555-567	13
α-helix	575-589	15
α-helix	601-606	6
α-helix	608-611	4
α-helix	614-624	11
α-helix	625-627	3
α-helix	637-654	18
α-helix	656-668	13
α-helix	670-684	15
α-helix	687-704	18
α-helix	722-752	31
α-helix	756-759	4
α-helix	765-780	16
α-helix	782-785	4
α-helix	792-795	4
α-helix	799-813	15
α-helix	817-825	9
α-helix	832-842	11
α-helix	852-878	27
α-helix	883-885	3
β-strand	886	1	3
β-strand	893	1	3
α-helix	894	1
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
α-helix	934	1
β-strand	935-936	2	4
α-helix	938-950	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin conjugation factor E4	A	protein	982	Saccharomyces cerevisiae	P54860 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2QIZ_1 Ubiquitin conjugation factor E4 (chains A)
GSHMASMTGGQQMGRGSEFRSMTAIEDILQITTDPSDTRGYSLLKSEEVPQGSTLGVDFI
DTLLLYQLTENEKLDKPFEYLNDCFRRNQQQKRITKNKPNAESLHSTFQEIDRLVIGYGV
VALQIENFCMNGAFINYITGIVSNVNSYTDFLSQIIQRAILEGTALDLLNAVFPTLLEYC
NKHVSHFDLNESVIYNNVLTIFELFVTFKPIAEIFTKIDGFFADYSCKPQDFERKTILGP
ILSLSPIEAAVAIRNYGDNLLRSKQQTAMIHESLQAEHKVVIDRLFFIVDKLVRGSLNSR
TDMISYFAHIANKNHLRRADHPPFKELSSNGFMSNITLLLVRFSQPFLDISYKKIDKIDA
NYFNNPSLFIDLSGETRLNSDFKEADAFYDKNRKTADSKPNFISDCFFLTLTYLHYGLGG
TLSFEEKMGSEIKALKEEIEKVKKIAANHDVFARFITAQLSKMEKALKTTESLRFALQGF
FAHRSLQLEVFDFICGASTFLIRVVDPEHEFPFKQIKLPLIPDQIGVENVDNADFLRAHA
PVPFKYYPEFVVEGPVNYSLYISKYQTSPIFRNPRLGSFVEFTTMVLRCPELVSNPHLKG
KLVQLLSVGAMPLTDNSPGFMMDIFEHDELVNKNLLYALLDFYVIVEKTGSSSQFYDKFN
SRYSISIILEELYYKIPSYKNQLIWQSQNNADFFVRFVARMLNDLTFLLDEGLSNLAEVH
NIQNELDNRARGAPPTREEEDKELQTRLASASRQAKSSCGLADKSMKLFEIYSKDIPAAF
VTPEIVYRLASMLNYNLESLVGPKCGELKVKDPQSYSFNPKDLLKALTTVYINLSEQSEF
ISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLLNFANKAEEQRKADEEEDLEYG
DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEE
LRQKILCFKKQKKEEAKHKASE

Primary citation

Inaugural Article: Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. Tu, D., Li, W., Ye, Y. et al. Proc Natl Acad Sci U S A (2007) 104:15599-15606. DOI 10.1073/pnas.0701369104 · 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
3M63 2.4 Å, Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2
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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