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- PDB-5jbv: Lys27-linked triubiquitin -

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Basic information

Entry
Database: PDB / ID: 5jbv
TitleLys27-linked triubiquitin
Components
  • D-ubiquitin
  • Ubiquitin
KeywordsPROTEIN BINDING / racemic crystal / synthetic protein / ubiquitin chains
Function / homology
Function and homology information


response to insecticide / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 ...response to insecticide / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / 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 / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / cytosolic ribosome / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Regulation of signaling by CBL / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR2 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Degradation of DVL
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
NITRATE ION / polypeptide(D) / polypeptide(D) (> 10) / Tail fiber / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.104 Å
AuthorsPan, M. / Gao, S. / Zheng, Y.
CitationJournal: To Be Published
Title: Structure of Lys27-linked triubiquitin
Authors: Pan, M. / Gao, S. / Zheng, Y.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 9, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: D-ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2674
Polymers17,1432
Non-polymers1242
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint2 kcal/mol
Surface area8070 Å2
Unit cell
Length a, b, c (Å)51.758, 51.758, 138.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-243-

HOH

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47, UniProt: P62987*PLUS
#2: Protein D-ubiquitin


Mass: 8565.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62987*PLUS
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.92 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.104→22.565 Å / Num. obs: 10189 / % possible obs: 85.8 % / Redundancy: 2.5 % / Net I/σ(I): 7.01

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 2.104→22.565 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 42.92
RfactorNum. reflection% reflection
Rfree0.3061 485 4.76 %
Rwork0.2611 --
obs0.2634 10189 63.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.104→22.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 8 71 1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021182
X-RAY DIFFRACTIONf_angle_d0.6341589
X-RAY DIFFRACTIONf_dihedral_angle_d15.985463
X-RAY DIFFRACTIONf_chiral_restr0.035190
X-RAY DIFFRACTIONf_plane_restr0.002205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1039-2.4080.3902780.34031475X-RAY DIFFRACTION29
2.408-3.03270.34412080.32854049X-RAY DIFFRACTION79
3.0327-22.56580.28091990.22734180X-RAY DIFFRACTION82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10960.0673-0.1890.3060.02290.23740.0945-0.34680.0093-0.0411-0.58210.20640.0568-1.58980.02650.16520.00130.13360.14680.36530.348-18.231410.35094.1484
20.00280.0123-0.01890.03050.09880.21310.2655-0.96690.68030.4498-0.30460.4686-0.0283-0.0740.10940.27360.10450.31890.52390.150.7922-19.29787.43899.6313
30.8594-0.4050.41550.1654-0.25870.85490.01460.07160.8421.25930.17910.0278-1.13820.3244-0.12690.36930.08750.06120.2923-0.01580.3634-10.799516.7589.1575
40.8144-0.10220.7520.4007-0.02921.0525-0.6769-0.4114-0.4612-0.1960.24980.0258-0.3095-0.3167-0.12220.22750.00470.12150.44050.04350.3684-9.01687.223214.1779
50.1949-0.0109-0.10280.1306-0.12810.0493-0.16360.1549-0.1480.13340.07780.2357-0.40970.2865-0.00140.313-0.0398-0.06090.3010.02840.2282-4.04639.36422.7212
60.04910.0592-0.020.13150.11410.13670.18260.03620.8503-0.1993-0.23910.0375-0.4945-0.251600.31410.01660.02670.2998-0.03620.2562-11.403413.2861-3.0778
70.0276-0.0283-0.06050.0411-0.02820.02680.0801-0.404-0.4238-0.1647-0.23060.65180.8499-0.1046-0.00030.39160.01280.00430.296-0.01910.3704-12.59993.88287.4341
80.02150.0032-0.01690.04180.04920.0433-0.2015-0.30320.4254-0.3196-0.12090.5897-0.35750.3253-00.7661-0.154-0.09920.7880.09860.56-6.5527-1.686914.7583
90.65540.0754-0.39630.82670.00280.7702-0.1480.01670.1501-0.3472-0.01890.0565-0.0426-0.1519-0.00080.2938-0.0039-0.01710.29510.02980.2397-15.0694-3.4486-14.5232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 44 )
5X-RAY DIFFRACTION5chain 'A' and (resid 45 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 65 )
7X-RAY DIFFRACTION7chain 'A' and (resid 66 through 71 )
8X-RAY DIFFRACTION8chain 'A' and (resid 72 through 76 )
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 53 )

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