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- PDB-7tb1: Crystal structure of STUB1 with a macrocyclic peptide -

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Basic information

Entry
Database: PDB / ID: 7tb1
TitleCrystal structure of STUB1 with a macrocyclic peptide
Components
  • ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY
  • E3 ubiquitin-protein ligase CHIP
KeywordsTRANSFERASE / E3 Ligase / carboxy-terminus of Hsp70-interacting protein
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / positive regulation of ERAD pathway / ERBB2 signaling pathway / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / ubiquitin conjugating enzyme complex / misfolded protein binding / nuclear inclusion body / cellular response to misfolded protein ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / positive regulation of ERAD pathway / ERBB2 signaling pathway / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / ubiquitin conjugating enzyme complex / misfolded protein binding / nuclear inclusion body / cellular response to misfolded protein / protein folding chaperone complex / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / chaperone-mediated autophagy / TPR domain binding / protein quality control for misfolded or incompletely synthesized proteins / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / positive regulation of proteolysis / protein K63-linked ubiquitination / protein maturation / protein autoubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / Hsp70 protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / response to ischemia / G protein-coupled receptor binding / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / Regulation of necroptotic cell death / kinase binding / Downregulation of ERBB2 signaling / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / MAPK cascade / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / cellular response to heat / protein-macromolecule adaptor activity / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
1,3-bis(sulfanyl)propan-2-one / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 Å
AuthorsBahmanjah, S. / Klein, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Structure-Based Design of Macrocyclic Peptides Targeting STUB1.
Authors: Ng, S. / Brueckner, A.C. / Bahmanjah, S. / Deng, Q. / Johnston, J.M. / Ge, L. / Duggal, R. / Habulihaz, B. / Barlock, B. / Ha, S. / Sadruddin, A. / Yeo, C. / Strickland, C. / Peier, A. / ...Authors: Ng, S. / Brueckner, A.C. / Bahmanjah, S. / Deng, Q. / Johnston, J.M. / Ge, L. / Duggal, R. / Habulihaz, B. / Barlock, B. / Ha, S. / Sadruddin, A. / Yeo, C. / Strickland, C. / Peier, A. / Henry, B. / Sherer, E.C. / Partridge, A.W.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
B: E3 ubiquitin-protein ligase CHIP
C: ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY
D: ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9066
Polymers33,6624
Non-polymers2442
Water4,810267
1
A: E3 ubiquitin-protein ligase CHIP
D: ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9533
Polymers16,8312
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area7660 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
C: ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9533
Polymers16,8312
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.011, 77.602, 46.354
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 ubiquitin-protein ligase CHIP / Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / ...Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / RING-type E3 ubiquitin transferase CHIP / STIP1 homology and U box-containing protein 1


Mass: 15792.862 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STUB1, CHIP, PP1131 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Protein/peptide ALA-CYS-SER-SER-ILE-TRP-CYS-PRO-ASP-GLY


Mass: 1038.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct
#3: Chemical ChemComp-I1J / 1,3-bis(sulfanyl)propan-2-one


Mass: 122.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6OS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 3 M NaCl, 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.785→46.31 Å / Num. obs: 23936 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.995 / Net I/σ(I): 8.4
Reflection shellResolution: 1.785→1.816 Å / Num. unique obs: 1193 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-DEC-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6efk

6efk


Resolution: 1.785→46.31 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.864 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1185 4.95 %RANDOM
Rwork0.2239 ---
obs0.2267 23932 98.8 %-
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 24.27 Å2 / Biso min: 10.35 Å2
Baniso -1Baniso -2Baniso -3
1--14.442 Å20 Å20.0994 Å2
2--8.5146 Å20 Å2
3---5.9274 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.785→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 12 267 2452
Biso mean--26.91 32.32 -
Num. residues----273
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d816SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes394HARMONIC8
X-RAY DIFFRACTIONt_it2245HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2448SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2245HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3020HARMONIC20.83
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion16.91
LS refinement shellResolution: 1.785→1.8 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3822 32 6.68 %
Rwork0.2877 447 -
obs--96.27 %

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