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- PDB-8e7o: CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN -

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Basic information

Entry
Database: PDB / ID: 8e7o
TitleCRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN
Components(Ubiquitin) x 2
KeywordsSIGNALING PROTEIN / Degradation / Polypeptide / Homeostasis / Post-translational modification / Polyubiquitin chain
Function / homology
Function and homology information


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 ...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 / 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 / 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 / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Assembly Of The HIV Virion
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / 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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLemma, B.E. / Fushman, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065334 United States
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation.
Authors: Lemma, B. / Zhang, D. / Vamisetti, G.B. / Wentz, B.G. / Suga, H. / Brik, A. / Lubkowski, J. / Fushman, D.
History
DepositionAug 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7208
Polymers34,3354
Non-polymers3844
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-64 kcal/mol
Surface area14390 Å2
Unit cell
Length a, b, c (Å)58.839, 77.164, 135.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 76 / Label seq-ID: 1 - 76

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 25% w/v PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→67.911 Å / Num. obs: 34404 / % possible obs: 99.3 % / Redundancy: 7.8 % / CC1/2: 1 / Net I/σ(I): 1.27
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.3 % / Num. unique obs: 1754 / CC1/2: 0.355 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAR

1aar


Resolution: 1.7→67.911 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.151 / SU B: 9.038 / SU ML: 0.117 / Average fsc free: 0.9433 / Average fsc work: 0.9616 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.108 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2206 1742 5.098 %
Rwork0.1567 32425 -
all0.16 --
obs-34167 99.265 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 50.053 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å20 Å2
2--0.338 Å2-0 Å2
3---0.272 Å2
Refinement stepCycle: LAST / Resolution: 1.7→67.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 20 160 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122449
X-RAY DIFFRACTIONr_angle_refined_deg2.191.6553291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2845300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.656517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33610495
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.03810109
X-RAY DIFFRACTIONr_chiral_restr0.1530.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021732
X-RAY DIFFRACTIONr_nbd_refined0.1480.2981
X-RAY DIFFRACTIONr_nbtor_refined0.2530.21572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2164
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.250
X-RAY DIFFRACTIONr_mcbond_it7.7214.3051212
X-RAY DIFFRACTIONr_mcangle_it8.0256.4571508
X-RAY DIFFRACTIONr_scbond_it15.475.2781237
X-RAY DIFFRACTIONr_scangle_it15.8697.5641783
X-RAY DIFFRACTIONr_lrange_it14.088109.9713543
X-RAY DIFFRACTIONr_rigid_bond_restr7.75332449
X-RAY DIFFRACTIONr_ncsr_local_group_10.1450.052082
X-RAY DIFFRACTIONr_ncsr_local_group_20.1040.052203
X-RAY DIFFRACTIONr_ncsr_local_group_30.1280.052122
X-RAY DIFFRACTIONr_ncsr_local_group_40.1350.052124
X-RAY DIFFRACTIONr_ncsr_local_group_50.1430.052096
X-RAY DIFFRACTIONr_ncsr_local_group_60.1290.052143
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.144920.05007
12AX-RAY DIFFRACTIONLocal ncs0.144920.05007
23AX-RAY DIFFRACTIONLocal ncs0.10440.05008
24AX-RAY DIFFRACTIONLocal ncs0.10440.05008
35AX-RAY DIFFRACTIONLocal ncs0.128170.05007
36AX-RAY DIFFRACTIONLocal ncs0.128170.05007
47AX-RAY DIFFRACTIONLocal ncs0.135170.05008
48AX-RAY DIFFRACTIONLocal ncs0.135170.05008
59AX-RAY DIFFRACTIONLocal ncs0.142950.05007
510AX-RAY DIFFRACTIONLocal ncs0.142950.05007
611AX-RAY DIFFRACTIONLocal ncs0.128890.05007
612AX-RAY DIFFRACTIONLocal ncs0.128890.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.4151290.41722580.41725050.8310.83995.28940.377
1.744-1.7920.3851260.37223040.37324570.8870.8998.90110.328
1.792-1.8440.3231120.3122690.31123810.9220.9251000.258
1.844-1.9010.3361050.25121860.25522980.9240.95599.69540.198
1.901-1.9630.271140.19421370.19822630.9520.97399.46970.142
1.963-2.0320.2711180.17720400.18322040.9550.9897.91290.136
2.032-2.1080.261040.15819810.16320850.960.9841000.121
2.108-2.1940.253940.15919180.16420130.9590.98499.95030.125
2.194-2.2920.2311040.14818480.15319550.9660.98699.84650.117
2.292-2.4030.223970.12417540.12918540.9680.99199.83820.098
2.403-2.5330.2441010.13316750.13917760.9640.9891000.112
2.533-2.6870.233710.14316210.14716940.9680.98799.88190.122
2.687-2.8720.334700.16714940.17415810.9350.98398.92470.151
2.872-3.1010.227830.16113900.16514740.9670.98499.93220.154
3.101-3.3970.247610.16313080.16713690.9610.9831000.167
3.397-3.7970.207760.14411660.14812430.9750.98799.91950.155
3.797-4.3820.17690.12310460.12511190.9830.99199.64250.139
4.382-5.3610.168480.1228990.1249500.9840.99299.68420.143
5.361-7.5580.244320.1667030.1697410.9770.98199.19030.192
7.558-67.9110.11270.1474250.1454520.9890.9811000.197

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