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- PDB-6w7z: RNF12 RING domain in complex with Ube2d2 -

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Basic information

Entry
Database: PDB / ID: 6w7z
TitleRNF12 RING domain in complex with Ube2d2
Components
  • E3 ubiquitin-protein ligase RLIM
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / RING E3 ligase / Ubiquitin / Ubiquitin conjugating enzyme / X-chromosome inactivation / RING
Function / homology
Function and homology information


random inactivation of X chromosome / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / transcription repressor complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment ...random inactivation of X chromosome / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / transcription repressor complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ring finger domain / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...Ring finger domain / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RLIM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMiddleton, A.J. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains.
Authors: Middleton, A.J. / Zhu, J. / Day, C.L.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: E3 ubiquitin-protein ligase RLIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5545
Polymers28,3312
Non-polymers2233
Water2,630146
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)48.441, 50.453, 54.375
Angle α, β, γ (deg.)90.000, 99.720, 90.000
Int Tables number4
Space group name H-MP1211

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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: 17188.605 Da / Num. of mol.: 1
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 (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase RLIM / LIM domain-interacting RING finger protein / RING finger LIM domain-binding protein / R-LIM / RING ...LIM domain-interacting RING finger protein / RING finger LIM domain-binding protein / R-LIM / RING finger protein 12 / RING-type E3 ubiquitin transferase RLIM / Renal carcinoma antigen NY-REN-43 / RNF12-RING


Mass: 11142.513 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RLIM, RNF12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NVW2, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 15-20% PEG 3350, 100-200 mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→47.74 Å / Num. obs: 24099 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Rrim(I) all: 0.08 / Net I/σ(I): 12.3 / Num. measured all: 99121
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.711 / Num. unique obs: 1405 / CC1/2: 0.813 / Rpim(I) all: 0.397 / Rrim(I) all: 0.817 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.5.29data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD-phased structure of RNF12-Ube2d2 (undeposited model)

Resolution: 1.8→47.74 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2108 1166 4.84 %
Rwork0.1779 --
obs0.1795 24081 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.99 Å2 / Biso mean: 34.9294 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 1.8→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 8 146 1911
Biso mean--38.28 39.52 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021861
X-RAY DIFFRACTIONf_angle_d0.532531
X-RAY DIFFRACTIONf_dihedral_angle_d2.4131567
X-RAY DIFFRACTIONf_chiral_restr0.041273
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.8820.34421360.27292842
1.882-1.98120.27521450.22142821
1.9812-2.10530.2381410.19812884
2.1053-2.26780.24331530.18582838
2.2678-2.4960.24061600.18712839
2.496-2.85710.24281470.19042876
2.8571-3.59920.21371310.17872887
3.5992-47.740.15231530.14752928
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)
12.97641.0004-1.84627.3436-0.25536.2127-0.1610.09190.13-0.0219-0.05271.0207-0.0138-0.48920.14990.2095-0.0017-0.00650.2162-0.0020.391378.0287.65177.151
26.3628-4.33415.06775.5831-3.82587.6588-0.1407-0.40170.07450.35510.3508-0.0849-0.1963-0.4771-0.1610.20160.0076-0.00380.2032-0.00560.279388.2177.62384.396
35.9486-0.43095.06671.3122-0.01685.4114-0.15560.1713-0.12170.06840.0521-0.1737-0.02420.1950.08030.13790.00280.04860.1078-0.00940.21594.8611.23481.381
48.63920.22321.11724.7427-4.42866.56840.18890.1735-0.5912-0.3195-0.129-0.32040.16720.311-0.06190.1390.00580.02520.1806-0.05320.3076102.582-3.22779.009
54.6745-0.06793.62391.24750.19823.3510.10080.0829-0.51480.0180.0453-0.15940.35310.0696-0.16660.2079-0.01540.03580.1635-0.01390.351489.558-5.61778.233
65.0573.9299-4.61615.3819-3.87665.92120.10380.2379-0.6673-0.61630.19050.06090.6737-0.2092-0.2490.31860.0599-0.0880.3178-0.08520.5004103.445-12.42979.385
74.5226-3.2841-0.1075.38251.37224.63680.0459-0.5877-0.58940.58240.5412-0.44490.58270.4554-0.47880.26240.0463-0.13690.28890.01880.4204107.825-7.79891.612
89.90284.20844.25812.21471.5492.1609-0.04281.17580.4209-1.2950.0686-0.23290.44110.0449-0.10250.52850.0250.03010.5759-0.04590.324579.166-8.60351.945
99.3416-6.6163-7.37359.3515.682810.07650.05540.8806-0.8863-0.2641-0.68891.2564-0.1111-1.12830.75070.2784-0.0856-0.09810.405-0.07930.453262.035-6.11462.672
104.73080.3631-0.98576.85-5.07696.1925-1.0254-0.7084-1.14390.24750.310.88470.7415-0.01210.64670.25820.02570.10960.2896-0.04330.453266.259-3.83272.429
112.0391-3.3121-7.49512.0161.94955.82810.0125-0.55870.2238-0.0868-0.04010.5893-0.29810.2993-0.03190.144-0.0218-0.03370.1923-0.02230.276674.2030.51471.058
125.8273-4.9270.30487.97420.90744.6330.21280.1777-0.1306-0.4805-0.30441.0898-0.0232-0.48860.10390.2011-0.0454-0.05570.2609-0.01490.372367.213-5.3165.207
137.5136-2.93891.26968.2607-1.61075.65520.05160.45330.0551-0.4513-0.0178-0.0559-0.09660.2134-0.01740.1994-0.05190.01790.1919-0.02750.136278.507-7.4263.098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:16 )A0 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:39 )A17 - 39
3X-RAY DIFFRACTION3( CHAIN A AND RESID 40:75 )A40 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:85 )A76 - 85
5X-RAY DIFFRACTION5( CHAIN A AND RESID 86:112 )A86 - 112
6X-RAY DIFFRACTION6( CHAIN A AND RESID 113:121 )A113 - 121
7X-RAY DIFFRACTION7( CHAIN A AND RESID 122:147 )A122 - 147
8X-RAY DIFFRACTION8( CHAIN B AND RESID 546:554 )B546 - 554
9X-RAY DIFFRACTION9( CHAIN B AND RESID 555:565 )B555 - 565
10X-RAY DIFFRACTION10( CHAIN B AND RESID 566:570 )B566 - 570
11X-RAY DIFFRACTION11( CHAIN B AND RESID 571:575 )B571 - 575
12X-RAY DIFFRACTION12( CHAIN B AND RESID 576:590 )B576 - 590
13X-RAY DIFFRACTION13( CHAIN B AND RESID 591:615 )B591 - 615

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