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- PDB-5o44: Crystal structure of unbranched mixed tri-Ubiquitin chain contain... -

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Basic information

Entry
Database: PDB / ID: 5o44
TitleCrystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages.
Components
  • (Polyubiquitin- ...) x 2
  • Ubiquitin
KeywordsSIGNALING PROTEIN / Mixed linkage Ubiquitin chain
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / 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 / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / 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) / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells
Similarity search - Function
Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin
Similarity search - Component
Biological speciesMusca domestica (house fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsPadala, P. / Isupov, M.N. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel
CitationJournal: J. Mol. Biol. / Year: 2017
Title: The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.
Authors: Padala, P. / Soudah, N. / Giladi, M. / Haitin, Y. / Isupov, M.N. / Wiener, R.
History
DepositionMay 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
C: Polyubiquitin-B
D: Polyubiquitin-B
B: Polyubiquitin-B
E: Ubiquitin
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,23018
Polymers51,2936
Non-polymers93712
Water68538
1
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Ubiquitin
hetero molecules

C: Polyubiquitin-B
D: Polyubiquitin-B
E: Ubiquitin
hetero molecules

A: Ubiquitin
B: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules

A: Ubiquitin
B: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,46036
Polymers102,58612
Non-polymers1,87524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation6_445x-y-1,x-1,z+1/61
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area22170 Å2
ΔGint-388 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.767, 110.767, 417.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23B
14A
24E
15A
25F
16C
26D
17C
27B
18C
28E
19C
29F
110D
210B
111D
211E
112D
212F
113B
213E
114B
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA1 - 731 - 73
21LEULEUCB1 - 731 - 73
12GLYGLYAA1 - 761 - 76
22GLYGLYDC1 - 761 - 76
13LEULEUAA1 - 731 - 73
23LEULEUBD1 - 731 - 73
14GLYGLYAA1 - 761 - 76
24GLYGLYEE1 - 761 - 76
15GLYGLYAA1 - 761 - 76
25GLYGLYFF1 - 761 - 76
16LEULEUCB1 - 731 - 73
26LEULEUDC1 - 731 - 73
17ARGARGCB1 - 741 - 74
27ARGARGBD1 - 741 - 74
18LEULEUCB1 - 731 - 73
28LEULEUEE1 - 731 - 73
19LEULEUCB1 - 731 - 73
29LEULEUFF1 - 731 - 73
110LEULEUDC1 - 731 - 73
210LEULEUBD1 - 731 - 73
111GLYGLYDC1 - 761 - 76
211GLYGLYEE1 - 761 - 76
112GLYGLYDC1 - 761 - 76
212GLYGLYFF1 - 761 - 76
113LEULEUBD1 - 731 - 73
213LEULEUEE1 - 731 - 73
114LEULEUBD1 - 731 - 73
214LEULEUFF1 - 731 - 73
115GLYGLYEE1 - 761 - 76
215GLYGLYFF1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein Ubiquitin


Mass: 8578.809 Da / Num. of mol.: 2 / Mutation: K48C, K63R.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45TR8

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Polyubiquitin- ... , 2 types, 4 molecules CBDF

#2: Protein Polyubiquitin-B


Mass: 8462.727 Da / Num. of mol.: 2 / Mutation: Deleted for Gly 75 and Gly 76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Polyubiquitin-B


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 3 types, 50 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 7.2 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3M MgSo4 and 100mM MES monohydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.14→104.25 Å / Num. obs: 27681 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.142 / Net I/σ(I): 9.7
Reflection shellResolution: 3.14→3.33 Å / Redundancy: 10 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 4350 / CC1/2: 0.675 / Rsym value: 2.081 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
DMphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B08

3b08


Resolution: 3.14→95.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.25405 1362 4.9 %RANDOM
Rwork0.21691 ---
obs0.21866 26195 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 135.247 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å22.36 Å20 Å2
2--4.72 Å20 Å2
3----15.31 Å2
Refinement stepCycle: 1 / Resolution: 3.14→95.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 48 38 3680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3762.0074940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.12925.181166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54215734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9561528
X-RAY DIFFRACTIONr_chiral_restr0.1290.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212628
X-RAY DIFFRACTIONr_gen_planes_other
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_it11.70513.1151802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.09219.6592242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.54313.6891868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined22.98514363
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43920.1
12C43920.1
21A43860.1
22D43860.1
31A43320.11
32B43320.11
41A44760.11
42E44760.11
51A44260.1
52F44260.1
61C45320.07
62D45320.07
71C46240.1
72B46240.1
81C44320.1
82E44320.1
91C44920.08
92F44920.08
101D44840.09
102B44840.09
111D44660.11
112E44660.11
121D46200.08
122F46200.08
131B43960.11
132E43960.11
141B45000.08
142F45000.08
151E44880.11
152F44880.11
LS refinement shellResolution: 3.14→3.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 90 -
Rwork0.469 1886 -
obs--99.7 %

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