[English] 日本語
Yorodumi
- PDB-4k1r: Crystal structure of Schizosaccharomyces pombe sst2 catalytic dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k1r
TitleCrystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin
Components
  • AMSH-like protease sst2
  • Polyubiquitin-C
KeywordsHYDROLASE / Helix-beta-helix sandwich / ubiquitin / deubiquitination / Zinc metalloprotease / cytosol / endosome
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKBKE / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of DVL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of AXIN / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 Å
AuthorsShrestha, R.K. / Das, C.
CitationJournal: Biochemistry / Year: 2014
Title: Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product.
Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,02422
Polymers61,9404
Non-polymers1,08418
Water4,107228
1
A: AMSH-like protease sst2
B: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,57412
Polymers30,9702
Non-polymers60410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-74 kcal/mol
Surface area12280 Å2
MethodPISA
2
C: AMSH-like protease sst2
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,45010
Polymers30,9702
Non-polymers4808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-81 kcal/mol
Surface area12310 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-189 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.292, 74.457, 139.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

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


Mass: 21981.732 Da / Num. of mol.: 2 / Fragment: catalytic domain (unp residues 246-436)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC19B12.10, sst2 / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Polyubiquitin-C / Ubiquitin


Mass: 8988.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0CG48

-
Non-polymers , 4 types, 246 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 74847 / Num. obs: 74731 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 17.17
Reflection shellResolution: 1.63→1.66 Å / % possible all: 96.1

-
Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREP(ccp4)phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.632→44.245 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 3766 5.04 %random
Rwork0.1951 ---
obs0.1961 74731 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.632→44.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 48 228 4476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064312
X-RAY DIFFRACTIONf_angle_d1.1125812
X-RAY DIFFRACTIONf_dihedral_angle_d13.1271634
X-RAY DIFFRACTIONf_chiral_restr0.073681
X-RAY DIFFRACTIONf_plane_restr0.006733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6318-1.65240.24051260.23322482X-RAY DIFFRACTION95
1.6524-1.67420.24891190.22432599X-RAY DIFFRACTION100
1.6742-1.69710.23651500.21492601X-RAY DIFFRACTION100
1.6971-1.72140.26311310.21232582X-RAY DIFFRACTION100
1.7214-1.74710.21611020.20442635X-RAY DIFFRACTION100
1.7471-1.77440.21431340.21622638X-RAY DIFFRACTION100
1.7744-1.80350.22881360.21052584X-RAY DIFFRACTION100
1.8035-1.83460.24141410.19962587X-RAY DIFFRACTION100
1.8346-1.86790.22551090.20352626X-RAY DIFFRACTION100
1.8679-1.90380.2471390.20162635X-RAY DIFFRACTION100
1.9038-1.94270.21431360.19322594X-RAY DIFFRACTION100
1.9427-1.98490.231330.18912609X-RAY DIFFRACTION100
1.9849-2.03110.23071540.19122614X-RAY DIFFRACTION100
2.0311-2.08190.20361460.19192621X-RAY DIFFRACTION100
2.0819-2.13820.24141450.19332613X-RAY DIFFRACTION100
2.1382-2.20110.24881530.19822600X-RAY DIFFRACTION100
2.2011-2.27220.22371550.1932604X-RAY DIFFRACTION100
2.2722-2.35340.22581570.19812625X-RAY DIFFRACTION100
2.3534-2.44760.2151310.20432610X-RAY DIFFRACTION100
2.4476-2.5590.24141540.20282633X-RAY DIFFRACTION100
2.559-2.69390.18711530.20412635X-RAY DIFFRACTION100
2.6939-2.86260.23361350.20872663X-RAY DIFFRACTION100
2.8626-3.08360.24331430.21652640X-RAY DIFFRACTION100
3.0836-3.39380.23591420.21492694X-RAY DIFFRACTION100
3.3938-3.88460.21071550.19482665X-RAY DIFFRACTION100
3.8846-4.89320.16431440.15372720X-RAY DIFFRACTION100
4.8932-44.26150.1621430.17282856X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more