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- PDB-7l97: Crystal structure of STAMBPL1 in complex with an engineered binder -

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Basic information

Entry
Database: PDB / ID: 7l97
TitleCrystal structure of STAMBPL1 in complex with an engineered binder
Components
  • AMSH-like protease
  • Ubiquitin variant
KeywordsPROTEIN BINDING / STAMBP1 / Ubv / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / cellular response to L-leucine / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / protein deubiquitination / positive regulation of TORC1 signaling / Metalloprotease DUBs / endosome / proteolysis ...Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / cellular response to L-leucine / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / protein deubiquitination / positive regulation of TORC1 signaling / Metalloprotease DUBs / endosome / proteolysis / metal ion binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsGuo, Y. / Dong, A. / Hou, F. / Li, Y. / Zhang, W. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1.
Authors: Guo, Y. / Liu, Q. / Mallette, E. / Caba, C. / Hou, F. / Fux, J. / LaPlante, G. / Dong, A. / Zhang, Q. / Zheng, H. / Tong, Y. / Zhang, W.
History
DepositionJan 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMSH-like protease
B: Ubiquitin variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,87810
Polymers28,4312
Non-polymers4478
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-75 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.709, 68.882, 57.329
Angle α, β, γ (deg.)90.000, 98.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein AMSH-like protease / AMSH-LP / STAM-binding protein-like 1


Mass: 19649.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAMBPL1, AMSHLP, KIAA1373 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96FJ0, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Ubiquitin variant


Mass: 8780.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 69 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.78 % / Mosaicity: 2.773 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 1500, 0.2M NaCl, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16078 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.063 / Rrim(I) all: 0.139 / Χ2: 0.994 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.40.77860.7690.4050.8140.62796.4
2.03-2.073.50.6517780.8090.3680.7520.64596.8
2.07-2.113.70.6318150.8380.3530.7270.65698.3
2.11-2.153.80.6377550.8460.3460.7290.72198.7
2.15-2.240.5818160.880.310.6610.6798.8
2.2-2.254.20.5228050.9020.2690.590.70998.8
2.25-2.314.40.457970.9380.230.5070.69799.3
2.31-2.374.50.4057780.9480.2050.4550.73198.9
2.37-2.444.50.3918220.9350.1970.4390.76999.2
2.44-2.524.70.3447920.9640.1720.3860.76999.5
2.52-2.614.70.2988090.9690.1490.3340.77899.3
2.61-2.714.70.2538110.9750.1260.2830.84799.4
2.71-2.844.70.217970.9770.1040.2350.88999.5
2.84-2.994.70.1668100.9790.0830.1860.93599.8
2.99-3.174.70.1288120.9890.0620.1421.199.8
3.17-3.424.70.1088030.990.0550.1221.24599.5
3.42-3.764.70.0878040.9920.0430.0981.39599.6
3.76-4.314.60.0758240.9930.0380.0841.56399.5
4.31-5.434.60.0698190.9940.0350.0781.534100
5.43-504.50.0758450.9910.0390.0842.02299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å38.05 Å
Translation2.01 Å38.05 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNR,1UBQ

2znr

1ubq


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.954 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 690 4.3 %RANDOM
Rwork0.1846 ---
obs0.1859 15388 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 37.279 Å2 / Biso min: 22.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0.27 Å2
2--3.7 Å20 Å2
3----2.68 Å2
Refinement stepCycle: final / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 22 61 2037
Biso mean--53.39 40.49 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192009
X-RAY DIFFRACTIONr_bond_other_d0.0020.021940
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9692722
X-RAY DIFFRACTIONr_angle_other_deg0.88134472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18924.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.555159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212226
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02433
LS refinement shellResolution: 2.014→2.066 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 52 -
Rwork0.259 1023 -
all-1075 -
obs--89.36 %

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