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- PDB-5ohv: K33-specific affimer bound to K33 diUb -

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Basic information

Entry
Database: PDB / ID: 5ohv
TitleK33-specific affimer bound to K33 diUb
Components
  • K33-specific affimer
  • Ubiquitin
KeywordsSIGNALING PROTEIN / ubiquitin / cystatin / affimer
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 / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / 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 / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53 / EGFR downregulation / Negative regulation of FGFR1 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Translesion Synthesis by POLH / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsMichel, M.A. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
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 18, 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: Ubiquitin
C: Ubiquitin
D: K33-specific affimer
B: K33-specific affimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,19010
Polymers43,6304
Non-polymers5616
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-58 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.288, 120.288, 69.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein K33-specific affimer


Mass: 13238.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 21% PEG 3350 200 mM Li2SO4 100 mM NaOAc pH 5.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→60.144 Å / Num. obs: 9294 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.237 / Net I/σ(I): 5
Reflection shellResolution: 3.8→3.936 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2 / CC1/2: 0.679 / % possible all: 100

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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: 2.801→60.144 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 362 3.9 %
Rwork0.174 --
obs0.1761 9291 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→60.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 34 15 2636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032657
X-RAY DIFFRACTIONf_angle_d0.7763581
X-RAY DIFFRACTIONf_dihedral_angle_d15.44983
X-RAY DIFFRACTIONf_chiral_restr0.031407
X-RAY DIFFRACTIONf_plane_restr0.003451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8006-3.20580.31231020.25252989X-RAY DIFFRACTION100
3.2058-4.03890.24241370.18022970X-RAY DIFFRACTION100
4.0389-60.15780.18521230.1472970X-RAY DIFFRACTION100
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)
16.82422.3481-1.48466.07354.28155.62770.1764-0.9239-0.64480.0526-0.13860.29120.9344-0.3332-0.00250.3513-0.0596-0.0310.54260.11390.3273-3.376210.9155-45.1609
22.0023-1.69961.14825.08264.65155.0155-0.16490.9956-0.1598-0.35670.48431.07822.79732.0471-0.45180.6898-0.0193-0.21990.61480.06240.5486.658211.0275-34.1249
38.87452.315-5.29259.6741.02593.8026-0.8892-0.8095-1.30120.62380.2177-0.55840.71690.76090.31050.49620.08710.00480.48070.1560.59928.03379.9144-45.567
47.2467-5.329-1.67297.64520.44315.45270.2923-0.49490.6405-0.01460.0941-1.6066-0.15890.7531-0.29710.4005-0.0355-0.02140.3745-0.00940.73056.638519.6668-45.7445
53.4064-2.9361-2.64689.2589-0.58753.2984-0.37440.2239-0.39520.25890.39280.3919-0.5104-0.549-0.04050.46110.0222-0.0430.67680.07960.55390.946117.2127-34.1291
62.07982.2676-0.33555.1546-2.33061.53310.7146-0.12310.8578-0.0641-0.0596-0.5366-1.93440.0780.39690.69170.01240.05230.30910.05460.58193.371319.5442-51.4335
73.44440.726-0.14674.07332.28267.9256-0.2393-0.1262-0.534-0.9948-0.0599-0.4381-1.12981.03910.17520.5918-0.01640.14240.43060.09110.3194.05222.6368-67.1611
83.88760.62290.137.4583.69277.6337-0.15290.4694-0.1438-1.45330.3551-0.7754-0.26640.9901-0.14150.8283-0.07830.30740.6674-0.04240.73028.529715.98-74.4599
94.54484.06766.32589.21124.04779.35810.72540.9326-0.75510.22160.5182-1.5220.5881.1144-1.29910.52990.14550.14290.5617-0.01820.88088.818310.8584-67.2442
108.50880.77920.74443.37782.31187.6840.34070.7116-0.6651-1.0504-0.00150.34180.4015-0.0313-0.31940.65730.161-0.03080.4161-0.07480.465-0.501612.7333-71.7457
117.5316-1.40373.02827.70242.04168.06850.5993-0.6455-0.65760.0939-0.4101-0.45990.8096-0.3714-0.10170.3795-0.00270.02660.39170.07980.4985-1.441113.7048-61.61
122.8240.0201-1.53576.1716-4.30378.82910.10151.41990.116-0.23690.18880.8412-0.4251-0.9467-0.03020.4910.0416-0.01410.79710.03160.5556-26.086521.1138-65.1715
131.90081.2143-1.13124.7031-0.83966.9224-0.3038-1.5011-0.25950.3159-0.026-0.66310.084-0.08230.60780.38650.13290.01250.5546-0.04150.5291-19.213317.5525-45.8072
144.99711.5457-1.09583.6910.8592.4934-0.35650.49750.324-0.41950.01170.33590.1085-0.55890.26390.47570.04260.00490.49610.04670.3422-20.772718.4602-57.0357
159.3887-2.1246-3.70622.1749-2.98467.9338-0.4445-0.75180.51061.26340.07260.7882-0.2399-0.36470.30460.8068-0.10070.02080.3858-0.07180.679-7.060639.7794-48.5016
161.39120.66211.03197.6252-1.64431.2553-0.0926-0.1420.18290.49540.01510.5364-0.4855-0.2254-0.02340.4760.03110.0390.41470.04630.3762-4.468541.5671-56.0996
174.14333.59452.97259.8764.07384.7041-0.12890.50.17760.0460.0223-0.0803-0.15350.0910.18950.36740.06410.05520.34480.04840.2268-4.449831.7135-56.4887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 34 )
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 54 )
5X-RAY DIFFRACTION5chain 'A' and (resid 55 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 74 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 11 )
8X-RAY DIFFRACTION8chain 'C' and (resid 12 through 22 )
9X-RAY DIFFRACTION9chain 'C' and (resid 23 through 34 )
10X-RAY DIFFRACTION10chain 'C' and (resid 35 through 65 )
11X-RAY DIFFRACTION11chain 'C' and (resid 66 through 74 )
12X-RAY DIFFRACTION12chain 'D' and (resid 34 through 62 )
13X-RAY DIFFRACTION13chain 'D' and (resid 63 through 73 )
14X-RAY DIFFRACTION14chain 'D' and (resid 74 through 121 )
15X-RAY DIFFRACTION15chain 'B' and (resid 35 through 52 )
16X-RAY DIFFRACTION16chain 'B' and (resid 53 through 104 )
17X-RAY DIFFRACTION17chain 'B' and (resid 105 through 121 )

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