9LE4: MIT-CD complex of STAMBP

Crystal structure of the MIT-CD complex of STAMBP. Determined by X-ray diffraction at 2.6 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,310
Mol. weight: 152.04 kDa
Ligands: ZN
Released: 11 Jun 2025

Explore 9LE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LE4 contains 59 α-helices and 52 β-strands across 8 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-22	12
α-helix	33-53	21
α-helix	56-68	13
α-helix	69-73	5
α-helix	74-76	3
α-helix	88-94	7
α-helix	95-99	5
α-helix	100-132	33

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	248-250	3
β-strand	251	1	1
β-strand	254	1	1
β-strand	256-260	5	2
α-helix	263-270	8
α-helix	272-276	5
β-strand	282-290	9	2
β-strand	293-301	9	2
β-strand	304-306	3	3
β-strand	311-313	3	3
α-helix	317-326	10
β-strand	329-336	8	2
α-helix	346-356	11
β-strand	363-368	6	2
β-strand	373-379	7	2
α-helix	381-389	9
β-strand	405-407	3	2
β-strand	411-414	4	2
β-strand	419-422	4	2

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	33-53	21
α-helix	56-68	13
α-helix	69-73	5
α-helix	74-76	3
α-helix	88-94	7
α-helix	95-99	5
α-helix	100-142	43

Chain D: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	247-250	4
β-strand	251	1	6
β-strand	254	1	6
β-strand	256-260	5	7
α-helix	263-270	8
α-helix	272-276	5
β-strand	282-290	9	7
β-strand	293-301	9	7
α-helix	302-303	2
β-strand	304-306	3	8
β-strand	311-313	3	8
α-helix	317-326	10
β-strand	329-336	8	7
α-helix	346-358	13
β-strand	363-368	6	7
β-strand	373-379	7	7
α-helix	381-387	7
β-strand	405-407	3	7
β-strand	411-414	4	7
β-strand	419-422	4	7

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-22	12
α-helix	34-53	20
α-helix	56-68	13
α-helix	69-73	5
α-helix	74-76	3
α-helix	88-94	7
α-helix	95-99	5
α-helix	100-145	46

Chain F: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	248-250	3
β-strand	251	1	4
β-strand	254	1	4
β-strand	256-260	5	2
α-helix	263-270	8
α-helix	272-276	5
β-strand	282-290	9	2
β-strand	293-301	9	2
β-strand	306	1	5
β-strand	311	1	5
α-helix	317-326	10
β-strand	329-336	8	2
α-helix	346-358	13
β-strand	363-368	6	2
β-strand	373-379	7	2
α-helix	381-389	9
β-strand	405-407	3	2
β-strand	411-414	4	2
β-strand	419-422	4	2

Chain G: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	33-53	21
α-helix	56-68	13
α-helix	69-73	5
α-helix	74-76	3
α-helix	88-94	7
α-helix	95-99	5
α-helix	100-138	39

Chain H: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	248-250	3
β-strand	251	1	9
β-strand	254	1	9
β-strand	256-260	5	10
α-helix	263-270	8
α-helix	272-277	6
β-strand	282-289	8	10
β-strand	293-301	9	10
α-helix	302-303	2
β-strand	304-306	3	11
β-strand	311-313	3	11
α-helix	317-326	10
α-helix	328	1
β-strand	329-336	8	10
α-helix	346-358	13
β-strand	363-368	6	10
β-strand	373-379	7	10
α-helix	381-389	9
β-strand	405-407	3	10
β-strand	411-414	4	10
β-strand	419-422	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
STAM-binding protein	A, C, E, G	protein	149	Homo sapiens	O95630 (AlphaFold model)
STAM-binding protein	B, D, F, H	protein	184	Homo sapiens	O95630 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>9LE4_1 STAM-binding protein (chains A, C, E, G)
GGSMSDHGDVSLPPEDRVRALSQLGSAVEVNEDIPPRRYFRSGVEIIRMASIYSEEGNIE
HAFILYNKYITLFIEKLPKHRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKE
YTEYNEEKKKEAEELARNMAIQQELEKEK

Sequence of entity 2 (B, D, F, H), FASTA

>9LE4_2 STAM-binding protein (chains B, D, F, H)
GGSNSESIPTIDGLRHVVVPGRLCPQFLQLASANTARGVETCGILCGKLMRNEFTITHVL
IPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLP
ESVAIVCSPKFQETGFFKLTDHGLEEISSCRQKGFHPHSKDPPLFCSCSHVTVVDRAVTI
TDLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (MES) are not listed.

Primary citation

The MIT domain of STAMBP autoinhibits its deubiquitination activity. Chen, Z., Wang, G., Zhang, Y. et al. Structure (2025) 33:1337. DOI 10.1016/j.str.2025.05.001 · PubMed

Other PDB entries of the same protein (UniProt O95630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RZV 1.67 Å, The Crystal Structure of a E280A Mutant of the Catalytic Domain of AMSH
2XZE 1.75 Å, Structural basis for AMSH-ESCRT-III CHMP3 interaction
3RZU 2.5 Å, The Crystal Structure of the Catalytic Domain of AMSH
5IXF Solution structure of the STAM2 SH3 with AMSH derived peptide complex

Browse structure collections

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