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- PDB-3axc: Crystal structure of linear diubiquitin -

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Basic information

Entry
Database: PDB / ID: 3axc
TitleCrystal structure of linear diubiquitin
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / NF kappa B signaling
Function / homology
Function and homology information


Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / 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 ...Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / 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) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / 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 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / 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 / 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 / Regulation of BACH1 activity / small-subunit processome / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (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 / 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 / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / 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 / Termination of translesion DNA synthesis / Peroxisomal protein import
Similarity search - Function
S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family ...S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRohaim, A. / Kawasaki, M. / Kato, R. / Dikic, I. / Wakatsuki, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of a compact conformation of linear diubiquitin
Authors: Rohaim, A. / Kawasaki, M. / Kato, R. / Dikic, I. / Wakatsuki, S.
History
DepositionApr 1, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3722
Polymers17,2801
Non-polymers921
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.261, 35.314, 35.841
Angle α, β, γ (deg.)91.79, 112.85, 112.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ubiquitin /


Mass: 17279.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Linear diubiquitin / Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.1M MgCl2, 30% Dioxane, 30% Isopropanol , pH 7.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→32.26 Å / Num. obs: 6959 / % possible obs: 97.42 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.19→2.244 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 2.19→32.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.216 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27798 325 4.8 %RANDOM
Rwork0.20614 ---
obs0.20933 6485 97.42 %-
all-10720 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.478 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å2-2.65 Å22.66 Å2
2---3.05 Å2-2.78 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.19→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 6 35 1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221201
X-RAY DIFFRACTIONr_angle_refined_deg1.50921616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68325.84953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62415245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.89157
X-RAY DIFFRACTIONr_chiral_restr0.110.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021859
X-RAY DIFFRACTIONr_mcbond_it0.6751.5740
X-RAY DIFFRACTIONr_mcangle_it1.26221209
X-RAY DIFFRACTIONr_scbond_it1.9973461
X-RAY DIFFRACTIONr_scangle_it3.4584.5407
LS refinement shellResolution: 2.187→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 21 -
Rwork0.241 450 -
obs--90.23 %
Refinement TLS params.Method: refined / Origin x: -3.4089 Å / Origin y: 9.4905 Å / Origin z: -9.3952 Å
111213212223313233
T0.1371 Å2-0.0176 Å20.0384 Å2-0.1114 Å2-0.0637 Å2--0.1511 Å2
L0.5482 °2-0.3073 °20.4975 °2-1.271 °2-1.508 °2--1.9345 °2
S0.0134 Å °0.0153 Å °-0.0974 Å °-0.0662 Å °0.0461 Å °-0.0009 Å °0.0236 Å °0.0519 Å °-0.0595 Å °

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