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- PDB-4ljq: Crystal structure of the catalytic core of E3 ligase HOIP -

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Basic information

Entry
Database: PDB / ID: 4ljq
TitleCrystal structure of the catalytic core of E3 ligase HOIP
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / RNF31 / ZIBRA / RING domain / Zinc finger / IBR domain / RBR ligase / E3 ligase / Ubiquitin / HOIL-1 / Sharpin
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair ...: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsStieglitz, B. / Rana, R.R. / Koliopoulos, M.G. / Morris-Davies, A.C. / Christodoulou, E. / Howell, S. / Brown, N.R. / Rittinger, K.
CitationJournal: Nature / Year: 2013
Title: Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP.
Authors: Stieglitz, B. / Rana, R.R. / Koliopoulos, M.G. / Morris-Davies, A.C. / Schaeffer, V. / Christodoulou, E. / Howell, S. / Brown, N.R. / Dikic, I. / Rittinger, K.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase RNF31
A: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,13922
Polymers100,9614
Non-polymers1,17718
Water77543
1
B: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5676
Polymers25,2401
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5676
Polymers25,2401
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5025
Polymers25,2401
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5025
Polymers25,2401
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,06911
Polymers50,4812
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-48 kcal/mol
Surface area20700 Å2
MethodPISA
6
A: E3 ubiquitin-protein ligase RNF31
hetero molecules

D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,06911
Polymers50,4812
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1870 Å2
ΔGint-45 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.209, 47.767, 111.145
Angle α, β, γ (deg.)101.390, 90.120, 98.920
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B858 - 1070
2010A858 - 1070
1020B858 - 1070
2020C858 - 1070
1030B859 - 1070
2030D859 - 1070
1040A858 - 1070
2040C858 - 1070
1050A859 - 1070
2050D859 - 1070
1060C859 - 1070
2060D859 - 1070

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 25240.346 Da / Num. of mol.: 4 / Fragment: Catalytic domain (unp residues 853-1072)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Plasmid: pET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 12000, 800 mM LiCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.45→29.6 Å / Num. all: 32557 / Num. obs: 30946 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.33 % / Biso Wilson estimate: 49.188 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.45-2.590.4732.64209747499171
2.59-2.770.3774.41309719339195.4
2.77-2.990.2776295138833195.7
2.99-3.270.1879.03289308097196.8
3.27-3.650.13511.78248067375195.9
3.65-4.210.09115.39224406410195.8
4.21-5.130.06517.88185575496195.5
5.13-7.140.06318.42144894268195.6
7.14-300.05321.4385192464194.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.45 Å / D res low: 29.61 Å / FOM : 0.389 / FOM acentric: 0.396 / FOM centric: 0 / Reflection: 30648 / Reflection acentric: 28521 / Reflection centric: 0

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
REFMAC5.8.0046refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→29.6 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.816 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2008 6.5 %RANDOM
Rwork0.2065 ---
all0.248 ---
obs0.2088 28941 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.4 Å2 / Biso mean: 49.3476 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.31 Å20.29 Å2
2---0.26 Å2-0.07 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 18 43 5913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195998
X-RAY DIFFRACTIONr_bond_other_d0.0070.025462
X-RAY DIFFRACTIONr_angle_refined_deg1.791.978134
X-RAY DIFFRACTIONr_angle_other_deg1.427312555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14723.654260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39715879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2091529
X-RAY DIFFRACTIONr_chiral_restr0.1090.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216795
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021390
X-RAY DIFFRACTIONr_mcbond_it4.1344.8053033
X-RAY DIFFRACTIONr_mcbond_other4.1344.8033032
X-RAY DIFFRACTIONr_mcangle_it6.3577.1733755
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B93680.12
12A93680.12
21B93920.13
22C93920.13
31B92720.12
32D92720.12
41A96070.11
42C96070.11
51A95420.11
52D95420.11
61C96740.11
62D96740.11
LS refinement shellResolution: 2.445→2.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 91 -
Rwork0.412 1249 -
all-1340 -
obs--55.37 %

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