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- PDB-4zft: Catalytic domain of Sst2 F403W mutant bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4zft
TitleCatalytic domain of Sst2 F403W mutant bound to ubiquitin
Components
  • AMSH-like protease sst2
  • Polyubiquitin-B
KeywordsHYDROLASE / helix-beta-helix sandwich / ubiquitin / Zinc metalloprotease / endosome
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein K63-linked deubiquitination / female meiosis I ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / protein K63-linked deubiquitination / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / cell division site / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsBueno, A.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1R01RR026273 United States
CitationJournal: To Be Published
Title: Structure of the catalytic domain of Sst2 mutant F403W bound to ubiquitin at 2.3 Angstroms
Authors: Bueno, A.N.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMSH-like protease sst2
B: Polyubiquitin-B
C: AMSH-like protease sst2
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59013
Polymers62,0184
Non-polymers5729
Water1,42379
1
A: AMSH-like protease sst2
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3267
Polymers31,0092
Non-polymers3175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-48 kcal/mol
Surface area11610 Å2
MethodPISA
2
C: AMSH-like protease sst2
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2646
Polymers31,0092
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-53 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.820, 89.397, 117.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AMSH-like protease sst2 / Suppressor of ste12 deletion protein 2


Mass: 22020.768 Da / Num. of mol.: 2 / Fragment: unp residues 245-435 / Mutation: F403W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: sst2, SPAC19B12.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Polyubiquitin-B


Mass: 8988.284 Da / Num. of mol.: 2 / Fragment: unp residues 77-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: (0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→71.3 Å / Num. all: 35242 / Num. obs: 27153 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 2.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K1R

4k1r


Resolution: 2.304→49.191 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1363 5.02 %RANDOM
Rwork0.1919 ---
obs0.1942 27153 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.304→49.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 24 79 4161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094155
X-RAY DIFFRACTIONf_angle_d1.1565627
X-RAY DIFFRACTIONf_dihedral_angle_d13.7791537
X-RAY DIFFRACTIONf_chiral_restr0.044666
X-RAY DIFFRACTIONf_plane_restr0.005711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3037-2.38610.34131270.28182450X-RAY DIFFRACTION97
2.3861-2.48160.33931260.26542557X-RAY DIFFRACTION100
2.4816-2.59450.35211480.25172541X-RAY DIFFRACTION100
2.5945-2.73130.25721370.24442552X-RAY DIFFRACTION100
2.7313-2.90240.28211420.23642535X-RAY DIFFRACTION100
2.9024-3.12650.29981280.23262581X-RAY DIFFRACTION100
3.1265-3.4410.27471290.20732603X-RAY DIFFRACTION100
3.441-3.93880.2941280.18222590X-RAY DIFFRACTION100
3.9388-4.96170.15061380.1422643X-RAY DIFFRACTION100
4.9617-49.20190.16661600.15692738X-RAY DIFFRACTION100

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