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- PDB-9le4: Crystal structure of the MIT-CD complex of STAMBP -

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Basic information

Entry
Database: PDB / ID: 9le4
TitleCrystal structure of the MIT-CD complex of STAMBP
Components(STAM-binding protein) x 2
KeywordsENDOCYTOSIS / STAMBP / Deubiquitinase / autoinhibition
Function / homology
Function and homology information


negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / cleavage furrow / mitotic cytokinesis ...negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / cleavage furrow / mitotic cytokinesis / protein deubiquitination / cell surface receptor signaling pathway via JAK-STAT / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Metalloprotease DUBs / early endosome / endosome / protein domain specific binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
STAM-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Z. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2025
Title: The MIT domain of STAMBP autoinhibits its deubiquitination activity.
Authors: Chen, Z. / Wang, G. / Zhang, Y. / Ding, J.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STAM-binding protein
B: STAM-binding protein
E: STAM-binding protein
F: STAM-binding protein
C: STAM-binding protein
D: STAM-binding protein
G: STAM-binding protein
H: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,03620
Polymers150,7328
Non-polymers1,30412
Water2,702150
1
A: STAM-binding protein
B: STAM-binding protein
C: STAM-binding protein
D: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,01810
Polymers75,3664
Non-polymers6526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: STAM-binding protein
F: STAM-binding protein
G: STAM-binding protein
H: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,01810
Polymers75,3664
Non-polymers6526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.349, 110.550, 270.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
STAM-binding protein / MIT / Associated molecule with the SH3 domain of STAM / Endosome-associated ubiquitin isopeptidase


Mass: 17363.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAMBP, AMSH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein
STAM-binding protein / CD / Associated molecule with the SH3 domain of STAM / Endosome-associated ubiquitin isopeptidase


Mass: 20319.104 Da / Num. of mol.: 4 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAMBP, AMSH / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES (pH 6.5) and 20 % (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 98798 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 53.19 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.063 / Rrim(I) all: 0.143 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6912 / CC1/2: 0.79 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→22.43 Å / SU ML: 0.3425 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1995 3.66 %
Rwork0.2176 52543 -
obs0.2185 54538 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→22.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10104 0 56 150 10310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012410360
X-RAY DIFFRACTIONf_angle_d1.665514001
X-RAY DIFFRACTIONf_chiral_restr0.09371570
X-RAY DIFFRACTIONf_plane_restr0.02451803
X-RAY DIFFRACTIONf_dihedral_angle_d15.11013981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.32381410.30433697X-RAY DIFFRACTION99.56
2.67-2.740.32711400.28793659X-RAY DIFFRACTION99.69
2.74-2.820.32851410.27653713X-RAY DIFFRACTION99.87
2.82-2.910.31031420.27923749X-RAY DIFFRACTION99.92
2.91-3.020.31441380.27673643X-RAY DIFFRACTION99.89
3.02-3.140.29271430.27373732X-RAY DIFFRACTION99.92
3.14-3.280.2921420.2613742X-RAY DIFFRACTION99.97
3.28-3.450.25991420.24513725X-RAY DIFFRACTION99.97
3.45-3.670.23721420.22253741X-RAY DIFFRACTION100
3.67-3.950.22221420.21143737X-RAY DIFFRACTION100
3.95-4.340.19391420.19823763X-RAY DIFFRACTION100
4.34-4.970.22891440.17663811X-RAY DIFFRACTION100
4.97-6.230.23151450.2023839X-RAY DIFFRACTION100
6.23-22.430.18521510.17493992X-RAY DIFFRACTION99.54

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