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- PDB-5ohl: K6-specific affimer bound to K6 diUb -

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Basic information

Entry
Database: PDB / ID: 5ohl
TitleK6-specific affimer bound to K6 diUb
Components
  • K6-specific affimer
  • Polyubiquitin-B
KeywordsSIGNALING PROTEIN / ubiquitin / cystatin
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / 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 / fat pad development / mitochondrion transport along microtubule / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / 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 / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / 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 / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling
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
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMichel, M.A. / Komander, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council309756 United Kingdom
Medical Research Council (United Kingdom)U105192732 United Kingdom
Lister Institute for Preventive Medicine United Kingdom
European Union283570 United Kingdom
CitationJournal: Mol. Cell / Year: 2017
Title: Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.
Authors: Michel, M.A. / Swatek, K.N. / Hospenthal, M.K. / Komander, D.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
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: K6-specific affimer
B: K6-specific affimer
C: K6-specific affimer
D: K6-specific affimer
E: K6-specific affimer
F: K6-specific affimer
G: K6-specific affimer
H: K6-specific affimer
I: Polyubiquitin-B
J: Polyubiquitin-B
K: Polyubiquitin-B
L: Polyubiquitin-B
M: Polyubiquitin-B
N: Polyubiquitin-B
O: Polyubiquitin-B
P: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,60221
Polymers174,39116
Non-polymers6,2115
Water1,892105
1
J: Polyubiquitin-B

A: K6-specific affimer
C: K6-specific affimer
K: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6905
Polymers43,5984
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
MethodPISA
2
A: K6-specific affimer
C: K6-specific affimer
K: Polyubiquitin-B
hetero molecules

J: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,6905
Polymers43,5984
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7480 Å2
ΔGint-45 kcal/mol
Surface area16750 Å2
MethodPISA
3
L: Polyubiquitin-B

B: K6-specific affimer
E: K6-specific affimer
N: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
MethodPISA
4
B: K6-specific affimer
E: K6-specific affimer
N: Polyubiquitin-B
hetero molecules

L: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area7230 Å2
ΔGint-47 kcal/mol
Surface area17360 Å2
MethodPISA
5
I: Polyubiquitin-B

D: K6-specific affimer
H: K6-specific affimer
M: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,5984
Polymers43,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
MethodPISA
6
D: K6-specific affimer
H: K6-specific affimer
M: Polyubiquitin-B

I: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)43,5984
Polymers43,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area7440 Å2
ΔGint-47 kcal/mol
Surface area17090 Å2
MethodPISA
7
F: K6-specific affimer
G: K6-specific affimer
O: Polyubiquitin-B
P: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers43,5984
Non-polymers3,0602
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-42 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.502, 69.672, 99.297
Angle α, β, γ (deg.)79.79, 79.76, 83.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
K6-specific affimer


Mass: 13221.985 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 8
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.5→48.23 Å / Num. obs: 53211 / % possible obs: 98.4 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.791 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 4N6U

1ubq

4n6u


Resolution: 2.5→48.23 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2268 2661 5 %
Rwork0.2001 --
obs0.2015 53198 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 57 105 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510714
X-RAY DIFFRACTIONf_angle_d0.99614391
X-RAY DIFFRACTIONf_dihedral_angle_d16.3614088
X-RAY DIFFRACTIONf_chiral_restr0.041626
X-RAY DIFFRACTIONf_plane_restr0.0041823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.36131210.29572627X-RAY DIFFRACTION97
2.5455-2.59440.36391650.28172615X-RAY DIFFRACTION98
2.5944-2.64740.31951200.27932675X-RAY DIFFRACTION98
2.6474-2.70490.37921280.26542656X-RAY DIFFRACTION98
2.7049-2.76790.29991280.25722675X-RAY DIFFRACTION98
2.7679-2.83710.28341430.25612664X-RAY DIFFRACTION99
2.8371-2.91380.28691560.26032639X-RAY DIFFRACTION98
2.9138-2.99950.29911350.24912626X-RAY DIFFRACTION98
2.9995-3.09630.28181370.25172684X-RAY DIFFRACTION99
3.0963-3.20690.28321270.23062708X-RAY DIFFRACTION98
3.2069-3.33530.23761400.22732640X-RAY DIFFRACTION98
3.3353-3.48710.24681290.2092675X-RAY DIFFRACTION98
3.4871-3.67080.24231420.20012668X-RAY DIFFRACTION99
3.6708-3.90070.2581620.19732643X-RAY DIFFRACTION99
3.9007-4.20180.16681480.16712635X-RAY DIFFRACTION99
4.2018-4.62430.15721400.15372708X-RAY DIFFRACTION99
4.6243-5.29270.16621390.15412664X-RAY DIFFRACTION99
5.2927-6.66550.22041340.19172686X-RAY DIFFRACTION99
6.6655-48.24090.17481670.16592649X-RAY DIFFRACTION99

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