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- PDB-2xew: Crystal structure of K11-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 2xew
TitleCrystal structure of K11-linked diubiquitin
ComponentsUBIQUITIN
KeywordsCELL CYCLE / PROTEIN DEGRADATION / PROTEASOME / DEUBIQUITINATION
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 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 / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / NF-kB is activated and signals survival / Regulation of PTEN localization / 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 / cytosolic ribosome / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / 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 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Defective CFTR causes cystic fibrosis
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBremm, A. / Freund, S.M.V. / Komander, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Lys11-Linked Ubiquitin Chains Adopt Compact Conformations and are Preferentially Hydrolyzed by the Deubiquitinase Cezanne
Authors: Bremm, A. / Freund, S.M.V. / Komander, D.
History
DepositionMay 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 31, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: UBIQUITIN
F: UBIQUITIN
G: UBIQUITIN
H: UBIQUITIN
I: UBIQUITIN
J: UBIQUITIN
K: UBIQUITIN
L: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,60338
Polymers102,92212
Non-polymers1,68226
Water11,728651
1
A: UBIQUITIN
B: UBIQUITIN
C: UBIQUITIN
D: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,91015
Polymers34,3074
Non-polymers60311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: UBIQUITIN
F: UBIQUITIN
G: UBIQUITIN
H: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8729
Polymers34,3074
Non-polymers5645
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
I: UBIQUITIN
J: UBIQUITIN
K: UBIQUITIN
L: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,82214
Polymers34,3074
Non-polymers51410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.230, 79.960, 221.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
UBIQUITIN /


Mass: 8576.831 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: UBIQUITIN POLYMER LINKED THROUGH LYS11 IN AN ISOPEPTIDE LINKAGE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 PLYSS / References: UniProt: P62988, UniProt: P0CG48*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 3.42 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 3.5 / Details: 3M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE PH3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 70577 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 24.22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 2.2→24.918 Å / SU ML: 0.32 / σ(F): 0.02 / Phase error: 27.53 / Stereochemistry target values: ML
Details: RESIDUES LACKING DISCERNIBLE ELECTRON DENSITY WERE MODELED WITH OCCUPANCY SET TO 0.00. ISOPEPTIDE BONDS BETWEEN LYS11 AND THE C-TERMINAL GLY76 OF NEIGHBORING MOLECULES ARE PRESENT IN THIS ENTRY.
RfactorNum. reflection% reflection
Rfree0.2515 3319 5 %
Rwork0.205 --
obs0.2073 65987 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.491 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0121 Å20 Å20 Å2
2--0.1218 Å2-0 Å2
3----0.1339 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 101 651 7867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057414
X-RAY DIFFRACTIONf_angle_d0.9789961
X-RAY DIFFRACTIONf_dihedral_angle_d17.4262968
X-RAY DIFFRACTIONf_chiral_restr0.061174
X-RAY DIFFRACTIONf_plane_restr0.0041294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.32762920.25475659X-RAY DIFFRACTION84
2.2786-2.36980.32623400.24635859X-RAY DIFFRACTION87
2.3698-2.47750.27533350.22486045X-RAY DIFFRACTION89
2.4775-2.6080.273020.20316173X-RAY DIFFRACTION91
2.608-2.77120.26283340.21216252X-RAY DIFFRACTION92
2.7712-2.98480.29783450.22466357X-RAY DIFFRACTION93
2.9848-3.28460.25433340.19396559X-RAY DIFFRACTION96
3.2846-3.75850.22433510.17276598X-RAY DIFFRACTION96
3.7585-4.730.19173570.16366569X-RAY DIFFRACTION95
4.73-24.91950.23273290.2136597X-RAY DIFFRACTION91
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)
12.5308-0.51410.36011.76760.39030.6123-0.2823-0.0979-0.18590.130.27970.05520.11830.03420.01270.07240.0260.06350.07450.00820.101988.7325-12.0543150.408
21.47491.5949-0.48882.1488-1.2491.41960.1536-0.03790.38670.0896-0.00690.2758-0.18820.1584-0.13390.0891-0.04560.06370.0755-0.01250.109964.7489-7.2215150.2267
32.0434-1.5621-1.5081.59460.97311.48950.18670.01760.2396-0.0634-0.0177-0.2525-0.0278-0.0078-0.06460.11490.08810.04210.0849-0.00680.11169.56916.7394150.41
40.95850.7456-0.08651.61080.85610.82660.111-0.05390.03130.07-0.0412-0.0788-0.06170.117-0.02450.1119-0.05350.04210.1014-0.01360.10793.712511.8621150.3931
53.67090.3899-2.59852.8894-1.06752.82950.13491.11850.5401-0.42340.1022-0.0633-0.3654-1.0442-0.31810.17570.15560.0780.36440.12780.134969.528316.7043124.9746
61.5554-0.66340.76132.0485-0.93110.73180.03460.4528-0.0681-0.5803-0.02870.1510.16420.0225-0.0420.2246-0.0903-0.01050.3520.00790.047664.9893-7.3957125.0103
71.1396-0.21540.55610.70050.1781.01170.0043-0.0202-0.120.0804-0.01780.06180.25580.01450.01510.21520.01040.07610.1852-0.00420.042689.226-11.8931125.345
81.036-0.2253-0.58560.746-0.00490.72240.0062-0.1920.13610.1030.0890.009-0.25630.2107-0.03870.1517-0.0825-0.00240.1266-0.02130.043694.031612.0035125.2487
91.4509-1.1851-0.22451.71870.22760.36830.12530.14890.2624-0.225-0.0935-0.0981-0.01050.0289-0.05740.06840.05070.04780.0597-0.0150.151352.027430.3693153.3029
102.10831.1192-0.570.98010.06041.0559-0.16910.18980.0857-0.10380.0782-0.0480.05250.15740.05990.0804-0.07710.10330.1224-0.00310.2151.628554.7509153.2808
111.16450.7116-0.41921.42550.41511.14580.1482-0.17380.0160.112-0.19780.0077-0.16780.083-0.11120.0793-0.04160.06610.05070.00610.151651.997954.3167178.4905
121.5625-0.826-0.11581.43690.77160.6609-0.0585-0.07050.16410.10590.13230.0889-0.05230.0707-0.08730.07720.00330.07050.0609-0.01110.130351.853930.0026178.7549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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