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- PDB-6w9a: RNF12 RING domain in complex with Ube2e2 -

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Basic information

Entry
Database: PDB / ID: 6w9a
TitleRNF12 RING domain in complex with Ube2e2
Components
  • E3 ubiquitin-protein ligase RLIM
  • Ubiquitin-conjugating enzyme E2 E2
KeywordsLIGASE / RING E3 ligase / Ubiquitin / Ubiquitin conjugating enzyme / X-chromosome inactivation / RING
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / random inactivation of X chromosome / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / transcription repressor complex ...ISG15 transferase activity / ISG15-protein conjugation / random inactivation of X chromosome / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / transcription repressor complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of DNA-templated transcription / DNA damage response / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) ...Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 E2 / E3 ubiquitin-protein ligase RLIM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 22, 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 1.3Oct 18, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,86810
Polymers61,4224
Non-polymers4466
Water50428
1
A: Ubiquitin-conjugating enzyme E2 E2
B: E3 ubiquitin-protein ligase RLIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9345
Polymers30,7112
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-conjugating enzyme E2 E2
D: E3 ubiquitin-protein ligase RLIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9345
Polymers30,7112
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.355, 81.355, 98.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 E2 / E2 ubiquitin-conjugating enzyme E2 / UbcH8 / Ubiquitin carrier protein E2 / Ubiquitin-protein ligase E2


Mass: 19667.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E2, UBCH8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96LR5, 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


Mass: 11043.381 Da / Num. of mol.: 2
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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 100 mM Na/K phosphate, 100 mM bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→40.68 Å / Num. obs: 32329 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 47.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.037 / Rrim(I) all: 0.089 / Net I/σ(I): 15.9 / Num. measured all: 188008
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.129 / Num. unique obs: 3171 / CC1/2: 0.629 / Rpim(I) all: 0.51 / Rrim(I) all: 1.239 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.29data scaling
PHASERphasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y6L

1y6l


Resolution: 2.3→40.296 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2186 1642 5.08 %
Rwork0.18 --
obs0.182 32301 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.71 Å2 / Biso mean: 62.9466 Å2 / Biso min: 28.22 Å2
Refinement stepCycle: final / Resolution: 2.3→40.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 16 28 3574
Biso mean--83.47 45.31 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083645
X-RAY DIFFRACTIONf_angle_d0.9594948
X-RAY DIFFRACTIONf_dihedral_angle_d4.7742515
X-RAY DIFFRACTIONf_chiral_restr0.051554
X-RAY DIFFRACTIONf_plane_restr0.006634
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3002-2.36790.35851520.27952557
2.3679-2.44430.32411040.26552596
2.4443-2.53160.27891020.23142592
2.5316-2.6330.26261680.22872518
2.633-2.75280.26371410.22392536
2.7528-2.89790.3486800.23362623
2.8979-3.07940.27731460.21982531
3.0794-3.3170.22051890.20772496
3.317-3.65060.24881150.18912611
3.6506-4.17840.20771440.14972518
4.1784-5.26250.1621550.13482549
5.2625-40.2960.17311460.14842532
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)
13.771-0.8563-0.87995.95983.44787.0161-0.0602-0.10090.5122-0.08910.20250.0133-0.82670.1408-0.14010.448-0.0037-0.02020.3353-0.02910.3459-87.863859.00423.9047
21.995-0.74011.7865.8474-1.032.7276-0.0149-0.16980.1507-0.0161-0.054-0.1462-0.44470.10550.03970.3974-0.05290.04390.3264-0.06010.2428-80.656146.968410.8388
32.3896-0.6263-0.33922.0383-2.9336.4006-0.0217-0.07530.2851-0.1978-0.2173-0.5643-0.6760.63460.21480.383-0.1203-0.02030.35680.00950.323-74.432752.17314.9857
45.5444-1.51824.14977.2344-0.54446.58160.3338-0.0981-0.7708-0.2185-0.153-0.25110.43470.3143-0.18390.3187-0.0070.09540.3537-0.04690.2462-73.933832.944413.4392
55.9791.5718-0.02058.16826.81586.0048-0.73270.0760.4956-0.16910.7576-1.045-1.62191.345-0.09361.2961-0.5025-0.36120.96740.08441.0065-63.353276.690410.5163
67.38511.59036.97426.84463.65648.5407-0.10870.26130.173-0.2869-0.1676-0.7301-0.9031.21530.51631.2935-0.4276-0.18340.60830.06880.7222-70.16478.6446-7.9569
72.93020.27740.66235.7373-0.98554.5713-0.1123-0.1140.22270.2569-0.3809-0.5861-1.08450.54510.43570.8994-0.3101-0.16730.50310.06070.585-70.806570.6537-1.1849
85.25592.9213-4.29526.2036-4.29467.3776-0.0075-0.49370.01380.54580.07620.1229-0.0640.226-0.05890.4251-0.00460.00610.3774-0.00390.265-98.508240.47933.7441
92.66150.8352-1.08225.4766-2.08124.06170.1701-0.07950.34610.1413-0.1140.7154-0.3401-0.5354-0.01830.30780.01870.02960.3598-0.07640.4519-106.538251.4534-3.4108
108.7337-1.66620.47714.6784-1.04676.7397-0.04910.27771.3782-0.5458-0.08150.6409-1.2394-0.92790.20190.62150.2390.03760.48440.01660.8099-110.436466.6262-10.0435
113.61423.67181.71317.5931-3.1226.9263-0.4893-1.0041-1.76590.80610.00951.12320.9994-2.05460.34760.8-0.39450.22051.02630.04232.0196-122.542623.6241-1.7815
120.62421.56590.26017.1216-0.84916.9074-0.86610.4523-0.7553-0.79570.60623.08060.9938-1.3210.01771.0217-0.3175-0.13130.6106-0.04651.8656-112.702716.2987-7.152
137.05954.2492-4.46762.7554-2.40644.84991.31370.2795-1.18970.1587-2.1563-0.16431.40260.90930.87690.9371-0.06470.31390.66480.00421.27-96.835917.4368-10.0948
148.8196-0.77230.46378.38440.16294.61310.05780.0684-0.9901-0.4908-0.1080.79860.7096-0.39050.04150.6328-0.19310.0370.3576-0.00570.6003-109.236726.3448-6.6708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 48:91)A48 - 91
2X-RAY DIFFRACTION2(chain A and resid 92:140)A92 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:166)A141 - 166
4X-RAY DIFFRACTION4(chain A and resid 167:201)A167 - 201
5X-RAY DIFFRACTION5(chain B and resid 546:553)B546 - 553
6X-RAY DIFFRACTION6(chain B and resid 554:566)B554 - 566
7X-RAY DIFFRACTION7(chain B and resid 567:615)B567 - 615
8X-RAY DIFFRACTION8(chain C and resid 48:88)C48 - 88
9X-RAY DIFFRACTION9(chain C and resid 89:165)C89 - 165
10X-RAY DIFFRACTION10(chain C and resid 166:201)C166 - 201
11X-RAY DIFFRACTION11(chain D and resid 546:553)D546 - 553
12X-RAY DIFFRACTION12(chain D and resid 554:560)D554 - 560
13X-RAY DIFFRACTION13(chain D and resid 561:567)D561 - 567
14X-RAY DIFFRACTION14(chain D and resid 568:615)D568 - 615

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