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- PDB-9yea: Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugat... -

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Basic information

Entry
Database: PDB / ID: 9yea
TitleStructure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin conjugating enzyme / ubiquitin / conjugate / isopeptide
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / 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 / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / 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 / activated TAK1 mediates p38 MAPK activation / 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 / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / 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 / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints
Similarity search - Function
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-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
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsManage, M.M. / Nix, J.C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128595 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Functional and structural analyses of UbcH5 mutants with enhanced binding to the E3 ubiquitin ligase CHIP
Authors: Manage, M.M. / Nix, J.C. / Page, R.C.
History
DepositionSep 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)25,7602
Polymers25,7602
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.445, 52.171, 52.337
Angle α, β, γ (deg.)90.000, 102.235, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17182.707 Da / Num. of mol.: 1 / Mutation: M1K, C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62837, 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: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Sodium Citrate, 20 % (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000002 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 1.83→36.52 Å / Num. obs: 35456 / % possible obs: 98.99 % / Redundancy: 6.89 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Net I/σ(I): 14.6
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1831 / CC1/2: 0.422 / Rpim(I) all: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→36.52 Å / SU ML: 0.3152 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.0219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 3543 10.01 %
Rwork0.1958 31862 -
obs0.2001 35405 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.95 Å2
Refinement stepCycle: LAST / Resolution: 1.83→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 66 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781786
X-RAY DIFFRACTIONf_angle_d0.95732442
X-RAY DIFFRACTIONf_chiral_restr0.0552279
X-RAY DIFFRACTIONf_plane_restr0.0092319
X-RAY DIFFRACTIONf_dihedral_angle_d13.3892661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.860.48031430.44131259X-RAY DIFFRACTION93.84
1.86-1.880.49031430.41241257X-RAY DIFFRACTION97.9
1.88-1.910.4371350.3891264X-RAY DIFFRACTION99.08
1.91-1.940.44981480.35761283X-RAY DIFFRACTION98.96
1.94-1.970.36371410.35761291X-RAY DIFFRACTION99.44
1.97-2.010.39171440.31371285X-RAY DIFFRACTION99.03
2.01-2.040.30661420.27871275X-RAY DIFFRACTION99.37
2.04-2.080.26291460.24931292X-RAY DIFFRACTION99.17
2.08-2.120.33071390.24351281X-RAY DIFFRACTION99.79
2.12-2.170.26551450.22131339X-RAY DIFFRACTION99.6
2.17-2.220.33931370.24531249X-RAY DIFFRACTION99.57
2.22-2.280.24161420.23291275X-RAY DIFFRACTION98.81
2.28-2.340.33071430.2231286X-RAY DIFFRACTION98.82
2.34-2.410.3061430.23021275X-RAY DIFFRACTION99.16
2.41-2.480.30251430.23041290X-RAY DIFFRACTION97.55
2.48-2.570.29721310.22971182X-RAY DIFFRACTION94.46
2.57-2.680.29691420.23651267X-RAY DIFFRACTION98.53
2.68-2.80.27061480.2171319X-RAY DIFFRACTION99.39
2.8-2.940.2341400.22311281X-RAY DIFFRACTION99.09
2.94-3.130.25091450.21431289X-RAY DIFFRACTION98.96
3.13-3.370.231390.18041248X-RAY DIFFRACTION97.95
3.37-3.710.20171420.16991304X-RAY DIFFRACTION98.77
3.71-4.240.19081410.13811243X-RAY DIFFRACTION97.67
4.25-5.340.17991360.14791235X-RAY DIFFRACTION94.55
5.35-36.520.19161450.1681293X-RAY DIFFRACTION99.72
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)
19.0686466603-3.884972880352.906784992969.401844952294.611039679556.08718446174-0.5010571811721.15590506925-0.1259958562690.5923229484880.2813126232260.0116967901392-0.6731107516741.463969338350.3143699656620.800535655891-0.2674446555940.1785678658440.922333710027-0.1064997553360.4440156013124.82374013371.41867510148-10.5192160429
29.313996931055.25816502821-2.829753089384.440198363591.235631591856.34445556014-0.2547372831950.282228486139-0.539758198452-1.114620230350.435115716569-1.07441825628-0.5826459894820.3152447193-0.04184481537050.57966415168-0.1044822093280.1515584419080.49220792367-0.1005603718730.49447351555414.4888891222-3.09067912206-11.0712849866
37.151499166822.89537704433-1.195238595374.778840814271.135190196454.50203622668-0.02531275909850.0008435732160890.402781395649-0.266190466264-0.0413535585874-0.0151798077506-0.3668342211640.2412424977320.08753383425770.3296553999450.0381521995298-0.00419004630960.2455008630190.02997187993880.2484655347517.89294169027-1.41727363016-2.16358368075
42.828028942631.62999208017-2.462956905263.699438323740.9323737213515.343119127420.128575675264-0.287480890612-0.137240290134-0.272408408140.0766625485241-0.27274065792-0.3784269182770.401001542845-0.2244819685790.4272136874720.0131101952619-0.02301668112570.3895149478930.00518188042530.42684445029215.8563697597-0.2054704681853.06015769838
57.32039913079-4.07372136933-4.396133813895.47183644495.654423632995.95566675262-0.247434427358-0.794429303375-0.2815352421261.721489507580.0840772675975-0.2881258573540.8053157425751.345048363530.3393399049510.5917610184240.0102635775359-0.04352492756150.4566468804610.1019028672670.4206494138275.06178353216-3.8185723274311.2617630878
65.486342705940.282666792431-1.423646206644.972876640432.192658829145.400144946330.02112409050120.00851305788664-0.3996725015420.394685315756-0.2709412133880.3558293154360.654032447733-0.9537227610130.2375731470740.420187731048-0.05485275045580.05149477540290.3363052137780.004046752749330.419022658888-4.17983759207-10.78085178666.05655313645
74.10040936217-1.84534399541-1.847086969579.524533631774.919066514783.09939261785-0.01869393516670.197159253751-0.1048968030830.3378906340140.1585858750040.9620157764150.778055151838-1.51674120511-0.1354723341860.517527281958-0.1628018759220.0008514165395110.665969241151-0.0329258461270.555773152713-16.66994995896.5099957901219.8281728659
87.57261670757-5.03001008412-4.726445261063.636862268874.506252630249.40865352918-0.684504523623-0.961725364359-0.5385659741920.9486801748380.353237309751-0.1362232494291.055397807420.464949035980.4054760637820.6820188294660.03114821152560.1296089620090.5676326436470.0109991744090.434847055172-9.478123179724.6720970390325.0661391097
99.45528383079-3.79871398206-4.708316274066.928038237041.04221899842.50208062624-0.180166206843-0.3730219374330.2183560098050.9685694521850.4068128791540.1262810181140.08139099924320.245933767348-0.2321282804250.5888523779090.03705505785870.002547131694320.4186116656760.01230572769980.345167921549-7.153369881811.499809794919.7508213962
107.235511709191.43861766735-3.419158293686.98731108252-1.99009276237.034428061880.1137578057580.3873074592120.4383970278150.359466137270.3403240526010.881489670529-0.661049066955-1.20440004607-0.4501621498380.5971935467090.06658487313350.06024231843320.5005503049020.1216809264020.448544758347-13.277127894313.252783492118.6431186834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 15 )AA0 - 151 - 16
22chain 'A' and (resid 16 through 38 )AA16 - 3817 - 39
33chain 'A' and (resid 39 through 84 )AA39 - 8440 - 85
44chain 'A' and (resid 85 through 110 )AA85 - 11086 - 111
55chain 'A' and (resid 111 through 120 )AA111 - 120112 - 121
66chain 'A' and (resid 121 through 147 )AA121 - 147122 - 148
77chain 'B' and (resid 1 through 22 )BB1 - 221 - 22
88chain 'B' and (resid 23 through 33 )BB23 - 3323 - 33
99chain 'B' and (resid 34 through 56 )BB34 - 5634 - 56
1010chain 'B' and (resid 57 through 72 )BB57 - 7257 - 72

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