[English] 日本語
Yorodumi
- PDB-3ifw: Crystal structure of the S18Y variant of ubiquitin carboxy termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ifw
TitleCrystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester.
Components
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase isozyme L1
Keywordshydrolase/hydrolase inhibitor / Enzyme-suicide substrate complex / Cytoplasm / Disease mutation / Glycoprotein / Hydrolase / Ligase / Oxidation / Polymorphism / Protease / Thiol protease / Ubl conjugation pathway / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / : / : / protein modification process => GO:0036211 / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / : / : / protein modification process => GO:0036211 / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein deubiquitination / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of macroautophagy / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of MAP kinase activity / Maturation of protein E / axon cytoplasm / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / positive regulation of glycolytic process / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / response to ischemia / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / 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
METHYL 4-AMINOBUTANOATE / Ubiquitin carboxyl-terminal hydrolase isozyme L1 / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDas, C. / Boudreaux, D. / Maiti, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
Authors: Boudreaux, D.A. / Maiti, T.K. / Davies, C.W. / Das, C.
History
DepositionJul 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9803
Polymers33,8632
Non-polymers1171
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.304, 87.304, 193.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

Detailsthe biological unit is a heterodimer consist of chain A and B in the asymmetric unit.

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L1 / UCH-L1 / Ubiquitin thioesterase L1 / Neuron cytoplasmic protein 9.5 / PGP 9.5 / PGP9.5


Mass: 25342.895 Da / Num. of mol.: 1 / Mutation: S18Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGP9.5, UCHL1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P09936, ubiquitinyl hydrolase 1, Ligases
#2: Protein Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBIQ_HUMAN
Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P62988, UniProt: P0CG48*PLUS
#3: Chemical ChemComp-GVE / METHYL 4-AMINOBUTANOATE


Type: peptide-like / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.4 M ammonium sulfate, 0.1M BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0032 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0032 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 11248 / Num. obs: 11248 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 21
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3 / Rsym value: 0.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ETL PDB ENTRY 1XD3, CHAIN B

2etl

1xd3


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 24.693 / SU ML: 0.269 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.762 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25627 539 4.8 %RANDOM
Rwork0.2089 ---
obs0.21105 10699 98.17 %-
all-11248 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 8 51 2403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8961.9753215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9235296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93325.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0561513
X-RAY DIFFRACTIONr_chiral_restr0.0540.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.21016
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21618
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1621.51531
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.28222382
X-RAY DIFFRACTIONr_scbond_it0.5073947
X-RAY DIFFRACTIONr_scangle_it0.7624.5833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 42 -
Rwork0.292 749 -
obs--96.46 %

+
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