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- PDB-5x0w: Molecular mechanism for the binding between Sharpin and HOIP -

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Basic information

Entry
Database: PDB / ID: 5x0w
TitleMolecular mechanism for the binding between Sharpin and HOIP
Components
  • E3 ubiquitin-protein ligase RNF31
  • Sharpin
KeywordsLIGASE/PROTEIN BINDING / Sharpin / HOIP / linear ubiquitination / E3 enzyme / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


apoptotic nuclear changes / regulation of CD40 signaling pathway / 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 ...apoptotic nuclear changes / regulation of CD40 signaling pathway / 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 / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / negative regulation of inflammatory response / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / synapse / dendrite / protein-containing complex binding / zinc ion binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Sharpin, PH domain / Sharpin PH domain / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain ...Sharpin, PH domain / Sharpin PH domain / : / : / : / : / : / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31 / Sharpin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLiu, J. / Li, F. / Cheng, X. / Pan, L.
Funding support China, 5items
OrganizationGrant numberCountry
National Basic Research Program of China2013CB836900 China
Science and Technology Commission of Shanghai Municipality15JC1400400 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB20000000 China
National Natural Science Foundation of China31500597 China
Science and Technology Commission of Shanghai Municipality15ZR1449100 China
CitationJournal: Cell Rep / Year: 2017
Title: Structural Insights into SHARPIN-Mediated Activation of HOIP for the Linear Ubiquitin Chain Assembly
Authors: Liu, J. / Wang, Y. / Gong, Y. / Fu, T. / Hu, S. / Zhou, Z. / Pan, L.
History
DepositionJan 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
E: E3 ubiquitin-protein ligase RNF31
G: E3 ubiquitin-protein ligase RNF31
B: Sharpin
D: Sharpin
F: Sharpin
H: Sharpin


Theoretical massNumber of molelcules
Total (without water)120,7018
Polymers120,7018
Non-polymers00
Water00
1
A: E3 ubiquitin-protein ligase RNF31
B: Sharpin


Theoretical massNumber of molelcules
Total (without water)30,1752
Polymers30,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase RNF31
D: Sharpin


Theoretical massNumber of molelcules
Total (without water)30,1752
Polymers30,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase RNF31
F: Sharpin


Theoretical massNumber of molelcules
Total (without water)30,1752
Polymers30,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: E3 ubiquitin-protein ligase RNF31
H: Sharpin


Theoretical massNumber of molelcules
Total (without water)30,1752
Polymers30,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.347, 101.347, 146.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 18828.414 Da / Num. of mol.: 4 / Fragment: UNP residues 480-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
Sharpin / Shank-associated RH domain-interacting protein / Shank-interacting protein-like 1 / hSIPL1


Mass: 11346.813 Da / Num. of mol.: 4 / Fragment: UNP residues 206-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHARPIN, SIPL1, PSEC0216 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0F6

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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: 3.61 Å3/Da / Density % sol: 65.93 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES (pH 7.3), 7% (w/v) PEG8000, 8% (v/v) ethylene glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9995→33.897 Å / Num. obs: 66810 / % possible obs: 99.86 % / Redundancy: 7.37 % / Net I/σ(I): 23.9
Reflection shellResolution: 2.9995→3.05 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.84 / Num. unique obs: 1681 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→33.895 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3023 3394 5.08 %
Rwork0.261 --
obs0.2632 66810 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→33.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 0 0 0 5914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036023
X-RAY DIFFRACTIONf_angle_d0.7428147
X-RAY DIFFRACTIONf_dihedral_angle_d15.6483510
X-RAY DIFFRACTIONf_chiral_restr0.045893
X-RAY DIFFRACTIONf_plane_restr0.0051082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9995-3.04230.58331100.53682272X-RAY DIFFRACTION85
3.0423-3.08770.5011260.43112518X-RAY DIFFRACTION92
3.0877-3.13590.38791460.38242652X-RAY DIFFRACTION100
3.1359-3.18730.36881440.35782666X-RAY DIFFRACTION98
3.1873-3.24220.34841600.32722558X-RAY DIFFRACTION100
3.2422-3.30110.371480.33972660X-RAY DIFFRACTION99
3.3011-3.36460.4291240.34842698X-RAY DIFFRACTION100
3.3646-3.43320.37521600.32892712X-RAY DIFFRACTION100
3.4332-3.50780.35981160.31472670X-RAY DIFFRACTION100
3.5078-3.58930.39631420.2952668X-RAY DIFFRACTION100
3.5893-3.67890.34211340.28682688X-RAY DIFFRACTION100
3.6789-3.77830.35421480.26832656X-RAY DIFFRACTION100
3.7783-3.88930.36281380.26722714X-RAY DIFFRACTION100
3.8893-4.01470.33991200.2662644X-RAY DIFFRACTION100
4.0147-4.15790.3041320.25542664X-RAY DIFFRACTION99
4.1579-4.32410.29741460.23352648X-RAY DIFFRACTION100
4.3241-4.52040.24611960.20952576X-RAY DIFFRACTION100
4.5204-4.75810.24411520.21632670X-RAY DIFFRACTION100
4.7581-5.05530.29561320.20972738X-RAY DIFFRACTION100
5.0553-5.44420.25751540.23692660X-RAY DIFFRACTION100
5.4442-5.98940.34011180.26832698X-RAY DIFFRACTION100
5.9894-6.84980.32471320.26772680X-RAY DIFFRACTION100
6.8498-8.60660.23121560.22592644X-RAY DIFFRACTION100
8.6066-33.8970.24491600.22662662X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 48.1572 Å / Origin y: 4.5246 Å / Origin z: 41.7853 Å
111213212223313233
T0.8445 Å20.1192 Å20.0422 Å2-0.5443 Å20.0255 Å2--0.5858 Å2
L0.0594 °20.0601 °20.2633 °2-0.2397 °2-0.7796 °2--0.4202 °2
S-0.063 Å °-0.0315 Å °-0.0198 Å °0.3004 Å °0.2722 Å °0.1789 Å °-0.2318 Å °-0.2898 Å °-0.2027 Å °
Refinement TLS groupSelection details: all

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