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- PDB-9q88: High-resolution structure of RNF38 RING domain -

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Basic information

Entry
Database: PDB / ID: 9q88
TitleHigh-resolution structure of RNF38 RING domain
ComponentsE3 ubiquitin-protein ligase RNF38
KeywordsLIGASE / Ubiquitination / E3 RING
Function / homology
Function and homology information


sperm flagellum / RING-type E3 ubiquitin transferase / male gonad development / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 23, 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 / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2663
Polymers9,1351
Non-polymers1312
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.820, 39.309, 53.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase RNF38 / RING finger protein 38 / RING-type E3 ubiquitin transferase RNF38


Mass: 9135.328 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.82 Å3/Da / Density % sol: 82.57 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Molecular Dimensions; 0.09 M Halogens, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→31.62 Å / Num. obs: 30264 / % possible obs: 80.04 % / Redundancy: 5.3 % / Biso Wilson estimate: 10.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Net I/σ(I): 18.1
Reflection shellResolution: 1.2→1.28 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 184 / CC1/2: 0.937 / Rpim(I) all: 0.51

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→31.62 Å / SU ML: 0.0659 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 1411 4.66 %RANDOM
Rwork0.1512 28853 --
obs0.152 30264 74.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.2→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 2 95 732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0103659
X-RAY DIFFRACTIONf_angle_d1.2132894
X-RAY DIFFRACTIONf_chiral_restr0.092396
X-RAY DIFFRACTIONf_plane_restr0.0082121
X-RAY DIFFRACTIONf_dihedral_angle_d6.296790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.259110.2509336X-RAY DIFFRACTION8.57
1.24-1.290.2424660.24061151X-RAY DIFFRACTION30.21
1.29-1.350.2249950.22321929X-RAY DIFFRACTION50.42
1.35-1.420.20341360.19132611X-RAY DIFFRACTION68.5
1.42-1.510.17461850.15553632X-RAY DIFFRACTION93.35
1.51-1.630.16971620.15243851X-RAY DIFFRACTION99.93
1.63-1.790.17051600.14213868X-RAY DIFFRACTION99.83
1.79-2.050.13912130.14763794X-RAY DIFFRACTION99.8
2.05-2.580.14561900.1493839X-RAY DIFFRACTION99.78
2.59-31.620.17961930.14173842X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 1.38072147722 Å / Origin y: -3.48336263032 Å / Origin z: -12.5142623246 Å
111213212223313233
T0.0949220204059 Å20.00478646906321 Å20.00876708371387 Å2-0.080270978755 Å2-0.00290206763436 Å2--0.0844177104917 Å2
L1.19450690187 °20.452405110346 °20.454899941448 °2-1.07520683159 °2-0.338354434594 °2--0.681333988961 °2
S-0.0253653331949 Å °-0.0315263937344 Å °-0.012924989685 Å °0.0197653101538 Å °-0.00462904003919 Å °-0.0271186644978 Å °0.0467395382718 Å °0.01615611354 Å °0.0461020009186 Å °
Refinement TLS groupSelection details: all

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