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- PDB-9q8y: Structure of RNF38 RING with linchpin mutant R454Y in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9q8y
TitleStructure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub
Components
  • Isoform 2 of E3 ubiquitin-protein ligase RNF38
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitination / linchpin / RING ligase
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / male gonad development / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Ring finger domain / 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 / S27a-like superfamily / Ring finger ...Ring finger domain / 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 / S27a-like superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RNF38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGabrielsen, M. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Life Sci Alliance / Year: 2025
Title: Tuning ubiquitin transfer by RING E3 ubiquitin ligases through the linchpin residue.
Authors: Nakasone, M.A. / Buetow, L. / Gabrielsen, M. / Ahmed, S.F. / Majorek, K.A. / Sibbet, G.J. / Smith, B.O. / Huang, D.T.
History
DepositionFeb 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin-conjugating enzyme E2 D2
C: Isoform 2 of E3 ubiquitin-protein ligase RNF38
D: Isoform 2 of E3 ubiquitin-protein ligase RNF38
F: Ubiquitin-40S ribosomal protein S27a
G: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,11210
Polymers66,8516
Non-polymers2624
Water905
1
A: Ubiquitin-conjugating enzyme E2 D2
C: Isoform 2 of E3 ubiquitin-protein ligase RNF38
F: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5565
Polymers33,4253
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 D2
D: Isoform 2 of E3 ubiquitin-protein ligase RNF38
G: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5565
Polymers33,4253
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.079, 116.079, 90.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,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: 16720.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue C85K forming a covalent bond to C-terminal Ubiquitin
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 Isoform 2 of E3 ubiquitin-protein ligase RNF38 / RING finger protein 38 / RING-type E3 ubiquitin transferase RNF38


Mass: 8041.210 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF38 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H0F5, RING-type E3 ubiquitin transferase
#3: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 8663.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3QTR3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Imidazole pH 8.0, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.63→43.92 Å / Num. obs: 40071 / % possible obs: 99 % / Redundancy: 10 % / Biso Wilson estimate: 80.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Net I/σ(I): 22.9
Reflection shellResolution: 2.63→2.77 Å / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 879 / CC1/2: 0.853 / Rpim(I) all: 0.308 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→43.92 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1948 4.86 %RANDOM
Rwork0.2317 ---
obs0.2338 40071 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 4 5 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234146
X-RAY DIFFRACTIONf_angle_d2.3755676
X-RAY DIFFRACTIONf_dihedral_angle_d6.554562
X-RAY DIFFRACTIONf_chiral_restr0.123658
X-RAY DIFFRACTIONf_plane_restr0.018741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.690.37771490.33412349X-RAY DIFFRACTION87
2.69-2.770.38691260.31352813X-RAY DIFFRACTION100
2.77-2.850.36141460.2862717X-RAY DIFFRACTION100
2.85-2.940.3087980.30662838X-RAY DIFFRACTION100
2.94-3.040.41511520.33152719X-RAY DIFFRACTION100
3.04-3.170.32371220.28642762X-RAY DIFFRACTION100
3.17-3.310.31261780.24672731X-RAY DIFFRACTION100
3.31-3.480.33341200.29462657X-RAY DIFFRACTION96
3.48-3.70.33361260.27732766X-RAY DIFFRACTION100
3.7-3.990.24871540.21612766X-RAY DIFFRACTION100
3.99-4.390.24041460.2112744X-RAY DIFFRACTION100
4.39-5.020.22321430.20592770X-RAY DIFFRACTION100
5.02-6.330.27531520.222731X-RAY DIFFRACTION100
6.33-43.920.24951360.19322760X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -24.9037 Å / Origin y: 74.1629 Å / Origin z: -9.7095 Å
111213212223313233
T0.7632 Å2-0.0865 Å2-0.11 Å2-0.5027 Å20.0024 Å2--0.5621 Å2
L2.4801 °20.9443 °2-0.0178 °2-2.2332 °20.9241 °2--0.9679 °2
S0.1086 Å °0.1053 Å °0.4282 Å °-0.1485 Å °-0.2251 Å °0.4409 Å °-0.4143 Å °-0.0792 Å °0.0641 Å °
Refinement TLS groupSelection details: all

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