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- PDB-7keo: Crystal structure of K29-linked di-ubiquitin in complex with synt... -

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Basic information

Entry
Database: PDB / ID: 7keo
TitleCrystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment
Components
  • Synthetic antigen binding fragment, heavy chain
  • Synthetic antigen binding fragment, light chain
  • Ubiquitin
KeywordsPROTEIN BINDING / protein complex
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 / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / 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 / Negative regulators of DDX58/IFIH1 signaling / 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 / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / EGFR downregulation / Activation of NF-kappaB in B cells / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G2/M Checkpoints / Iron uptake and transport / Hedgehog ligand biogenesis / Assembly Of The HIV Virion / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYu, Y. / Zheng, Q. / Erramilli, S. / Pan, M. / Kossiakoff, A. / Liu, L. / Zhao, M.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.
Authors: Yu, Y. / Zheng, Q. / Erramilli, S.K. / Pan, M. / Park, S. / Xie, Y. / Li, J. / Fei, J. / Kossiakoff, A.A. / Liu, L. / Zhao, M.
History
DepositionOct 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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

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Assembly

Deposited unit
A: Synthetic antigen binding fragment, heavy chain
B: Synthetic antigen binding fragment, light chain
C: Ubiquitin
D: Ubiquitin
E: Synthetic antigen binding fragment, heavy chain
F: Synthetic antigen binding fragment, light chain
G: Ubiquitin
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,63714
Polymers131,0678
Non-polymers5706
Water23413
1
A: Synthetic antigen binding fragment, heavy chain
B: Synthetic antigen binding fragment, light chain
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9138
Polymers65,5334
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Synthetic antigen binding fragment, heavy chain
F: Synthetic antigen binding fragment, light chain
G: Ubiquitin
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7236
Polymers65,5334
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.620, 43.740, 174.750
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Synthetic antigen binding fragment, heavy chain


Mass: 25022.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody Synthetic antigen binding fragment, light chain


Mass: 23356.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Protein
Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 4
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
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M phosphate-citriate, 40% v/v Polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.9→19.701 Å / Num. obs: 30022 / % possible obs: 98.1 % / Redundancy: 3.705 % / Biso Wilson estimate: 53.767 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.189 / Χ2: 0.987 / Net I/σ(I): 6.72 / Num. measured all: 111228 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.983.7140.9771.468004219521550.571.14198.2
2.98-3.063.6380.8111.77819218921490.6290.95198.2
3.06-3.153.8510.7232.098053212520910.7220.83998.4
3.15-3.243.6150.5332.647223203619980.8270.62698.1
3.24-3.353.8110.4763.27618203319990.840.55398.3
3.35-3.473.8090.3564.197138191218740.9360.41498
3.47-3.63.8630.2875.087200189818640.9580.33298.2
3.6-3.743.7580.2325.996595177917550.9720.2798.7
3.74-3.913.5480.1866.776089174817160.9710.21998.2
3.91-4.13.7750.1587.996131164716240.9820.18498.6
4.1-4.323.6030.1129.845631157615630.9880.13299.2
4.32-4.593.7540.08811.95530149214730.9950.10298.7
4.59-4.93.8330.08812.065404142614100.9940.10298.9
4.9-5.293.7330.08911.854849132212990.9950.10398.3
5.29-5.83.5790.10110.444270120211930.9930.11899.3
5.8-6.483.6410.1099.744005111511000.9920.12898.7
6.48-7.493.7090.08411.13368710039940.9950.09899.1
7.49-9.173.5580.05914.4229398388260.9960.06998.6
9.17-12.973.2460.04216.4421526716630.9980.0598.8
12.97-19.7013.2280.04614.918914032760.9970.05468.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: stripped Fab model

Resolution: 2.9→19.701 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2818 1500 5.01 %
Rwork0.2362 28464 -
obs0.2386 29964 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.94 Å2 / Biso mean: 62.3596 Å2 / Biso min: 33.65 Å2
Refinement stepCycle: final / Resolution: 2.9→19.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8846 0 30 13 8889
Biso mean--73.13 48.38 -
Num. residues----1177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.99310.37851330.3268251698
2.9931-3.09970.36081360.3313257698
3.0997-3.22330.34071320.3029251598
3.2233-3.36930.31931370.2833260098
3.3693-3.5460.33571340.28252798
3.546-3.76670.30971350.2537256198
3.7667-4.05520.33161370.2468260498
4.0552-4.4590.24031360.2048258899
4.459-5.09450.20391380.1866260899
5.0945-6.38210.261400.2186265899
6.3821-19.70.25761420.202271198

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