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- PDB-5bnb: Crystal structure of a Ube2S-ubiquitin conjugate -

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Basic information

Entry
Database: PDB / ID: 5bnb
TitleCrystal structure of a Ube2S-ubiquitin conjugate
Components
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 S
KeywordsCELL CYCLE / ubiquitin-conjugating enzyme / E2 enzyme / UBC domain / ubiquitination
Function / homology
Function and homology information


protein K29-linked ubiquitination / protein K27-linked ubiquitination / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / anaphase-promoting complex binding / protein K6-linked ubiquitination / positive regulation of ubiquitin protein ligase activity / exit from mitosis / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic 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 / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / 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 / 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
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin conserved site ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLorenz, S.G. / Feiler, C.G. / Kuriyan, J.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
The Leukemia and Lymphoma Society5509-11 United States
German Research FoundationLO 2003/1-1 Germany
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of a Ube2S-Ubiquitin Conjugate.
Authors: Lorenz, S. / Bhattacharyya, M. / Feiler, C. / Rape, M. / Kuriyan, J.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 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-conjugating enzyme E2 S
B: Ubiquitin-conjugating enzyme E2 S
C: Ubiquitin-conjugating enzyme E2 S
E: Polyubiquitin-B
F: Polyubiquitin-B
G: Polyubiquitin-B
I: Polyubiquitin-B
D: Ubiquitin-conjugating enzyme E2 S


Theoretical massNumber of molelcules
Total (without water)104,1608
Polymers104,1608
Non-polymers00
Water1,08160
1
A: Ubiquitin-conjugating enzyme E2 S
G: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)26,0402
Polymers26,0402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 S
I: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)26,0402
Polymers26,0402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 S
E: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)26,0402
Polymers26,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Polyubiquitin-B
D: Ubiquitin-conjugating enzyme E2 S


Theoretical massNumber of molelcules
Total (without water)26,0402
Polymers26,0402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.906, 45.854, 110.576
Angle α, β, γ (deg.)90.00, 93.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 S / E2-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin- ...E2-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin-conjugating enzyme E2-EPF5 / Ubiquitin-protein ligase S


Mass: 17417.012 Da / Num. of mol.: 4 / Mutation: C118M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2S, E2EPF, OK/SW-cl.73 / Plasmid: pSMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16763, ubiquitin-protein ligase
#2: Protein
Polyubiquitin-B


Mass: 8622.922 Da / Num. of mol.: 4 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: bar
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.49→47.38 Å / Num. obs: 32942 / % possible obs: 97.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.3
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.2 / % possible all: 95.3

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Processing

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

1zdn


Resolution: 2.49→47.382 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.304 1647 5 %
Rwork0.243 --
obs0.2462 32915 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→47.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 0 60 6235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026302
X-RAY DIFFRACTIONf_angle_d0.6298625
X-RAY DIFFRACTIONf_dihedral_angle_d11.232204
X-RAY DIFFRACTIONf_chiral_restr0.0261039
X-RAY DIFFRACTIONf_plane_restr0.0031132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.56330.36341460.30012446X-RAY DIFFRACTION92
2.5633-2.6460.39311420.29872611X-RAY DIFFRACTION99
2.646-2.74060.38351240.30132630X-RAY DIFFRACTION99
2.7406-2.85030.391600.27282650X-RAY DIFFRACTION99
2.8503-2.980.35061360.2692589X-RAY DIFFRACTION99
2.98-3.13710.34531330.25692665X-RAY DIFFRACTION99
3.1371-3.33360.36571090.2572666X-RAY DIFFRACTION99
3.3336-3.59090.29931210.24352603X-RAY DIFFRACTION97
3.5909-3.95210.32111350.23672580X-RAY DIFFRACTION96
3.9521-4.52360.25341470.21182612X-RAY DIFFRACTION97
4.5236-5.69780.24911290.22222615X-RAY DIFFRACTION96
5.6978-47.39050.28481650.2342601X-RAY DIFFRACTION93

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