7ZJU: SUMO-specific isopeptidase USPL1

Structure of human USPL1 in covalent complex with SUMO3-2Br probe. Determined by X-ray diffraction at 2.17 Å resolution. Released 27 Sept 2023.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,527
Mol. weight: 87.92 kDa
Ligands: ZN, OXU, CA
Released: 27 Sept 2023

Explore 7ZJU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZJU contains 24 α-helices and 44 β-strands across 4 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: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	227	1	1
α-helix	229-231	3
α-helix	236-246	11
α-helix	249-255	7
α-helix	265-277	13
α-helix	302-323	22
α-helix	333-341	9
α-helix	345-348	4
β-strand	353-360	8	2
β-strand	367-374	8	2
β-strand	377-379	3	3
β-strand	382	1	2
β-strand	387	1	4
β-strand	390	1	4
β-strand	391-395	5	2
β-strand	405-413	9	2
β-strand	417-422	6	3
α-helix	431-434	4
β-strand	436-438	3	3
β-strand	441-452	12	3
β-strand	456-462	7	3
β-strand	468-471	4	3
α-helix	473-475	3
β-strand	478	1	1
β-strand	480-482	3	3
α-helix	489-491	3
β-strand	492-499	8	3

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	5
β-strand	28-33	6	5
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	5
β-strand	64-65	2	5
β-strand	81-87	7	5

Chain C: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	227	1	6
α-helix	229-231	3
α-helix	236-246	11
α-helix	249-255	7
α-helix	265-282	18
α-helix	300-323	24
α-helix	333-342	10
α-helix	345-348	4
β-strand	353-360	8	7
β-strand	367-374	8	7
β-strand	377-379	3	8
β-strand	382	1	7
β-strand	387	1	9
β-strand	390	1	9
β-strand	391-395	5	7
β-strand	405-413	9	7
β-strand	417-422	6	8
α-helix	431-434	4
β-strand	436-438	3	8
β-strand	441-452	12	8
β-strand	456-462	7	8
β-strand	468-471	4	8
β-strand	478	1	6
β-strand	480-482	3	8
α-helix	489-491	3
β-strand	492-499	8	8

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	10
β-strand	28-33	6	10
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	10
β-strand	64-65	2	10
α-helix	72-75	4
β-strand	82-87	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-specific isopeptidase USPL1	A, C	protein	287	Homo sapiens	Q5W0Q7 (AlphaFold model)
Small ubiquitin-related modifier 3	B, D	protein	90	Homo sapiens	P55854 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7ZJU_1 SUMO-specific isopeptidase USPL1 (chains A, C)
GPCTSFPQALCVQWKNAYALCWLDCILSALVHSEELKNTVTGLCSKEESIFWRLLTKYNQ
ANTLLYTSQLSGVKDGDCKKLTSEIFAEIETCLNEVRDEIFISLQPQLRCTLGDMESPVF
AFPLLLKLETHIEKLFLYSFSWDFECSQCGHQYQNRHMKSLVTFTNVIPEWHPLNAAHFG
PCNNCNSKSQIRKMVLEKVSPIFMLHFVEGLPQNDLQHYAFHFEGCLYQITSVIQYRANN
HFITWILDADGSWLECDDLKGPCSERHKKFEVPASEIHIVIWERKIS

Sequence of entity 2 (B, D), FASTA

>7ZJU_2 Small ubiquitin-related modifier 3 (chains B, D)
SEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRF
DGQPINETDTPAQLEMEDEDTIDVFQQQTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
OXU	2-bromanylethanamine	C2 H6 Br N	2
CA	Calcium ion	Ca	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. Zhao, Z., O'Dea, R., Wendrich, K. et al. J Am Chem Soc (2023) 145:20801-20812. DOI 10.1021/jacs.3c04062 · PubMed

Other PDB entries of the same protein (UniProt Q5W0Q7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P99 1.8 Å, Structure of human USPL1 in complex with SUMO2
7ZJV 2.4 Å, Structure of human USPL1 in covalent complex with DeltaN-SUMO2/3-PA probe

Browse structure collections

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