[English] 日本語
Yorodumi
- PDB-4zfr: Catalytic domain of Sst2 F403A mutant bound to ubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zfr
TitleCatalytic domain of Sst2 F403A mutant bound to ubiquitin
Components
  • AMSH-like protease sst2
  • ubiquitin
KeywordsHYDROLASE / Helix- beta- helix sandwich / ubiquitin / Zinc metalloprotease / cytosol / endosome
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / 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 / late endosome to vacuole transport / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / 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 / late endosome to vacuole transport / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / protein K63-linked deubiquitination / mitochondrion transport along microtubule / K63-linked polyubiquitin modification-dependent protein binding / metal-dependent deubiquitinase activity / cell division site / K63-linked deubiquitinase activity / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / neuron projection morphogenesis / 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 / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / regulation of neuron apoptotic process / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / positive regulation of protein ubiquitination / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / ubiquitin binding / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB 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. / : / 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: 1.72 Å
AuthorsShrestha, R.K.
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 Catalytic domain of Sst2 F403A mutant bound to ubiquitin at 1.7 Angstroms
Authors: Shrestha, R.K.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMSH-like protease sst2
B: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1496
Polymers30,8942
Non-polymers2554
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-49 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.139, 58.174, 56.442
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 21905.637 Da / Num. of mol.: 1 / Fragment: unp residues 245-435 / Mutation: F403A
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-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 ubiquitin


Mass: 8988.284 Da / Num. of mol.: 1 / Fragment: unp residues 77-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol

-
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: Jun 30, 2014
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: 1.719→53.27 Å / Num. obs: 26060 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 23.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.32 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K1R

4k1r


Resolution: 1.72→53.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.593 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1382 5 %RANDOM
Rwork0.201 ---
obs0.203 26060 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→53.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 10 43 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192073
X-RAY DIFFRACTIONr_bond_other_d0.0020.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9722812
X-RAY DIFFRACTIONr_angle_other_deg0.88134715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53424.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.62159
X-RAY DIFFRACTIONr_chiral_restr0.1140.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2092.3461047
X-RAY DIFFRACTIONr_mcbond_other2.2082.3451046
X-RAY DIFFRACTIONr_mcangle_it2.8973.5091307
X-RAY DIFFRACTIONr_mcangle_other2.8963.511308
X-RAY DIFFRACTIONr_scbond_it2.8382.6171026
X-RAY DIFFRACTIONr_scbond_other2.8372.6171026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0753.8021506
X-RAY DIFFRACTIONr_long_range_B_refined5.84918.3442167
X-RAY DIFFRACTIONr_long_range_B_other5.84918.3532168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 87 -
Rwork0.29 1939 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: 17.428 Å / Origin y: 1.54 Å / Origin z: 17.376 Å
111213212223313233
T0.2211 Å2-0.0224 Å20.1177 Å2-0.0268 Å20.0053 Å2--0.0976 Å2
L1.3242 °20.2492 °20.1086 °2-3.8626 °20.1226 °2--2.0001 °2
S-0.1152 Å °0.094 Å °-0.031 Å °0.2188 Å °-0.0324 Å °-0.1791 Å °0.1066 Å °0.1446 Å °0.1476 Å °

+
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