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- PDB-7m4o: Crystal structure of phosphorylated RBR E3 ligase RNF216 in compl... -

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Basic information

Entry
Database: PDB / ID: 7m4o
TitleCrystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin
Components
  • E3 ubiquitin-protein ligase RNF216
  • Ubiquitin
KeywordsLIGASE / E3 ligase / RBR / ubiquitin / enzyme
Function / homology
Function and homology information


regulation of interferon-beta production / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / 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 ...regulation of interferon-beta production / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / 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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / protein K48-linked ubiquitination / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Degradation of AXIN / Hh mutants are degraded by ERAD / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Activation of NF-kappaB in B cells / Iron uptake and transport
Similarity search - Function
: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : ...: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase RNF216
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsCotton, T.R. / Lechtenberg, B.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1182757 Australia
CitationJournal: Mol.Cell / Year: 2022
Title: Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.
Authors: Cotton, T.R. / Cobbold, S.A. / Bernardini, J.P. / Richardson, L.W. / Wang, X.S. / Lechtenberg, B.C.
History
DepositionMar 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF216
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,88813
Polymers33,0083
Non-polymers88110
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, Kd = 24 microM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.526, 84.216, 90.095
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

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Protein , 2 types, 3 molecules ABC

#1: Protein E3 ubiquitin-protein ligase RNF216 / RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing ...RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing protein 3 / Ubiquitin-conjugating enzyme 7-interacting protein 1 / Zinc finger protein inhibiting NF-kappa-B


Mass: 15853.939 Da / Num. of mol.: 1 / Mutation: C688A
Source method: isolated from a genetically manipulated source
Details: Serine 719 is phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: RNF216, TRIAD3, UBCE7IP1, ZIN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NWF9, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: K63-linked di-ubiquitin; C-terminus of chain B conjugated to Lys63 of chain C via an isopeptide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48

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Non-polymers , 5 types, 91 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.22
Details: 0.259 M ammonium sulfate, 30.1 % PEG monomethyl ether 2000, 0.1M sodium acetate-acetic acid pH 5.22

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2.21→45.05 Å / Num. obs: 16539 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.08 / Rrim(I) all: 0.154 / Χ2: 0.54 / Net I/σ(I): 7.7
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1375 / CC1/2: 0.793 / Rpim(I) all: 0.594 / Rrim(I) all: 1.132 / Χ2: 0.48 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M4N

7m4n


Resolution: 2.21→45.05 Å / SU ML: 0.3032 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2519 1646 9.99 %
Rwork0.2008 14835 -
obs0.2059 16481 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.76 Å2
Refinement stepCycle: LAST / Resolution: 2.21→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 44 81 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032181
X-RAY DIFFRACTIONf_angle_d0.53422918
X-RAY DIFFRACTIONf_chiral_restr0.0426321
X-RAY DIFFRACTIONf_plane_restr0.0052376
X-RAY DIFFRACTIONf_dihedral_angle_d14.5137868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.33721380.27681172X-RAY DIFFRACTION97.54
2.27-2.340.33091310.25341216X-RAY DIFFRACTION99.93
2.34-2.430.3311380.25991216X-RAY DIFFRACTION100
2.43-2.530.31091220.25671218X-RAY DIFFRACTION100
2.53-2.640.30211470.22951215X-RAY DIFFRACTION99.78
2.64-2.780.25411270.22841244X-RAY DIFFRACTION99.85
2.78-2.950.29161360.23841224X-RAY DIFFRACTION99.71
2.95-3.180.27351410.22451219X-RAY DIFFRACTION100
3.18-3.50.25251340.18361260X-RAY DIFFRACTION99.93
3.5-4.010.22221380.17981227X-RAY DIFFRACTION100
4.01-5.050.2071450.15311271X-RAY DIFFRACTION99.93
5.05-45.050.22131490.18621353X-RAY DIFFRACTION99.73
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)
11.415882790840.452306731932-0.2077725121260.765961264043-0.4258079485420.235222136363-0.01240799833320.004259601544250.1756413531260.0273975215499-0.005337774853010.174157853160.02638775145950.0136915718086-0.001011771655280.3629523857030.0392294145772-0.02877091755860.333006870984-0.04230091999590.387825499371-12.376537985811.5829993747-16.7791222301
21.52912128533-0.203960604556-0.04750671041940.876729476721-0.421244094261.26426950976-0.0626192694015-0.211695062796-0.1127067951880.1257174576050.0276824007595-0.2474287010770.07172848283810.212729732649-8.17342571376E-60.364576265780.0163556653622-0.01998257590240.341527402877-0.02086828580750.3638801789635.0131941469715.5364716838-9.46009240729
30.9915238832170.10220671955-0.2666840742911.000626858640.4204646948490.7943530995650.116358419516-0.0637395940689-0.07356485078860.0904806205378-0.00101955983842-0.154829753715-0.08747297556030.06197454614934.92151397742E-50.343753118198-0.00945587879335-0.02613541088640.323712956215-0.00177556787650.384981573494-18.5379133379-21.1924289934-15.1780192202
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 652 through 771)AA652 - 7711 - 116
22(chain 'B' and resid 1 through 76)BH1 - 761 - 76
33(chain 'C' and resid 1 through 76)CN1 - 761 - 76

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