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- PDB-5tut: UbcH5a-Ub isopeptide conjugate -

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Basic information

Entry
Database: PDB / ID: 5tut
TitleUbcH5a-Ub isopeptide conjugate
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsTRANSFERASE / E2 conjugating enzyme
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / 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 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...positive regulation of protein polyubiquitination / 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 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / energy homeostasis / regulation of neuron apoptotic process / negative regulation of TORC1 signaling / 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
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsSanchez, J.G. / Wagner, J.M. / Pornillos, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM112508 United States
CitationJournal: To be Published
Title: UbcH5a-Ub isopeptide conjugate
Authors: Sanchez, J.G. / Wagner, J.M. / Pornillos, O.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)25,5072
Polymers25,5072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-3 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.949, 51.410, 53.157
Angle α, β, γ (deg.)90.00, 101.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D1 / UbcH5A / (E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / ...UbcH5A / (E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 16930.322 Da / Num. of mol.: 1 / Mutation: C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51668, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47

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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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growMethod: vapor diffusion, sitting drop / Details: Hampton PEG/Ion F10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6719 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.92 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.2 / Num. unique all: 554 / CC1/2: 0.872 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2C4P & 1UBQ

2c4p

1ubq


Resolution: 2.604→32.113 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2426 684 10.2 %
Rwork0.2002 --
obs0.2047 6708 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.604→32.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 0 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031838
X-RAY DIFFRACTIONf_angle_d0.5962494
X-RAY DIFFRACTIONf_dihedral_angle_d9.9941124
X-RAY DIFFRACTIONf_chiral_restr0.042276
X-RAY DIFFRACTIONf_plane_restr0.004323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6044-2.80530.31231230.271068X-RAY DIFFRACTION85
2.8053-3.08740.34561430.26231197X-RAY DIFFRACTION99
3.0874-3.53370.30261140.22871265X-RAY DIFFRACTION100
3.5337-4.45020.2091440.16551235X-RAY DIFFRACTION100
4.4502-32.11590.17821600.16261259X-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)
10.526-0.13720.050.49670.3890.3861-0.03760.0307-0.02070.04920.01760.0466-0.0293-0.0244-00.2160.0036-0.02640.19620.01120.22735.4821-0.368925.0272
20.18460.00790.05840.01660.00110.389-0.2868-0.0215-0.15590.05130.01890.03970.1658-0.2158-0.00020.3143-0.02340.04890.3541-0.02820.287-17.714411.293545.9221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 147)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 76)

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