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- PDB-8k6p: Crystal structure of SHARPIN LTM motif -

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Basic information

Entry
Database: PDB / ID: 8k6p
TitleCrystal structure of SHARPIN LTM motif
ComponentsSharpin
KeywordsPROTEIN BINDING / SHARPIN / LTM / homodimer
Function / homology
Function and homology information


apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization ...apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / negative regulation of inflammatory response / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / synapse / dendrite / protein-containing complex binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Sharpin, PH domain / Sharpin PH domain / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYan, Z. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753113 China
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN.
Authors: Zhang, Y. / Xu, X. / Wang, Y. / Wang, Y. / Zhou, X. / Pan, L.
#1: Journal: To Be Published
Title: Crystal structure of SHARPIN LTM motif.
Authors: Yan, Z. / Pan, L.F.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sharpin
B: Sharpin
C: Sharpin


Theoretical massNumber of molelcules
Total (without water)14,9393
Polymers14,9393
Non-polymers00
Water21612
1
A: Sharpin
B: Sharpin


Theoretical massNumber of molelcules
Total (without water)9,9592
Polymers9,9592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-21 kcal/mol
Surface area5470 Å2
MethodPISA
2
C: Sharpin

C: Sharpin


Theoretical massNumber of molelcules
Total (without water)9,9592
Polymers9,9592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2550 Å2
ΔGint-21 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.380, 39.240, 31.350
Angle α, β, γ (deg.)90.000, 97.041, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide Sharpin / Shank-associated RH domain-interacting protein / Shank-interacting protein-like 1 / hSIPL1


Mass: 4979.568 Da / Num. of mol.: 3 / Fragment: LTM motif
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate, and 2.0 M ammonium sulfate (pH 4.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.86→36.46 Å / Num. obs: 9723 / % possible obs: 98.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.994 / Net I/σ(I): 10
Reflection shellResolution: 1.86→1.92 Å / Num. unique obs: 866 / CC1/2: 0.622 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→25.2 Å / SU ML: 0.2539 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 43.4
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 458 4.71 %
Rwork0.218 9265 -
obs0.2208 9723 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.95 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 12 990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053990
X-RAY DIFFRACTIONf_angle_d0.66541334
X-RAY DIFFRACTIONf_chiral_restr0.0432159
X-RAY DIFFRACTIONf_plane_restr0.0039180
X-RAY DIFFRACTIONf_dihedral_angle_d33.0258365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-2.130.43251330.30992926X-RAY DIFFRACTION91.42
2.13-2.680.31631550.263138X-RAY DIFFRACTION97.17
2.69-25.20.24681700.19133201X-RAY DIFFRACTION97.74
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)
18.904232316110.267211861617-0.0320217683798.76590817134-2.052442520028.14977111993-0.004675044224311.479911894670.138121039299-0.3556709578530.172147404122-0.325214763096-0.833402048326-0.305424320848-0.194978095920.2593897312080.02704758469250.01744746991320.457592090570.02039746020530.3261234541215.2319594696-7.691828537593.61130499882
28.50005133442-2.90247907817-3.168110003227.109821448786.070032510049.167673410650.3209447557240.486385918243-1.20832128663-0.0790196243808-0.2549448046580.1710492030580.531674047877-0.3468384727790.04495676746730.2674973559560.0219422123573-0.03931106408180.270022574525-0.03188273174310.48970529610710.8231261696-17.15815733666.625462485
32.225651666134.116424124452.735097757658.58765926185.770850299013.83917394655-0.5165795783541.02285666555-0.162493812459-0.7178863626260.4223679915310.0599172656257-0.3384315924091.425914947690.4083826476250.4494831869350.2154183641680.04339655897781.010540640020.01915615318140.51311066969922.8524816896-14.22123043273.22326600676
49.32012979711.90304975182-6.236887851596.85559729688-1.854311424914.25629629010.3178306667691.900617444420.732965801089-0.733159277697-0.037537896961-0.916349584115-0.5495009409960.376816166217-0.2474754979990.4796906912380.0446913882097-0.008333133702930.7074020620460.07260335852520.4402580216936.4908004404-21.245683571113.0976539329
55.85597613981-1.308371875285.851710466266.49004573673-1.825338070415.982865212950.1739219983130.764915682662-0.8928526842280.159205548259-0.195559759756-0.007804885985860.1703585603560.337058852182-0.05495754465630.3339635006010.05831606513110.02287523639510.556617653903-0.08979705620890.59815407005724.3352933885-20.76413765899.0320726828
69.384682711271.828428842315.566686676569.002996473714.775220643354.925742521050.6452153643550.484543449316-2.229430642940.03449176313640.0248188992819-0.1383451968930.662179620716-0.327402080561-0.8361551132210.3730844243770.00513772295794-0.02722424654720.383267756183-0.1292315672860.70207244614515.5046292684-22.046026207310.3788961188
77.781854355862.01151237251-3.885406979886.82131590166-4.402317570895.9435285808-0.4333631680790.901869979655-0.00429807663172-0.1581487943550.147552125184-0.989504467336-0.5472058939380.5676829622440.1679659050020.38519553466-0.104652477671-0.003573946975880.434005183551-0.05057998302890.44466178451421.4377978653-10.85993733149.99297735238
82.903573864862.284271180842.572405634498.89755133465-0.3831510815133.12150858467-0.203866231110.3524027811230.583610264777-0.0205371353629-0.0695462757881-1.48463764099-1.658508283821.977356816830.4624059464260.597463609453-0.278051777825-0.06466175376130.9431863288550.0700142025710.52721564358115.72527485750.3484668266588.37793816281
98.679274409541.413562052645.268917972666.647632152271.535068404733.32221550983-0.06857701493210.4812487514750.448949448709-0.0414480547082-0.107826242262-0.262908133562-0.4780139546171.033153330680.1815689556240.27208756899-0.02066959206130.03209968042790.4001484940390.009376033984720.3243111619717.4673775894-5.580774647611.47207680408
108.8074611068-3.3850413047-0.5130312328977.22698169819-0.7167041870489.07120679540.178776002060.352736587354-0.556512913151-0.0823091720165-0.4552873926260.0008988646527310.6175258532680.686741203180.12589694480.229667993886-0.0195620784173-0.01176798631380.3998429022950.007622953662630.3314889113553.52833897715-13.49835609642.10433209277
118.83053595977-4.050094105952.963107003928.49271159667-3.915978737952.516873803430.132273580253-0.09036470497570.6699531772670.2982247591310.2498361850320.243781018175-0.7488982535050.5418269514410.29612282290.39872796985-0.04884020132270.007583113063920.423038441421-0.03755464150340.349066462868-1.74986635815-1.069620168682.18508295227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 168 through 185 )
2X-RAY DIFFRACTION2chain 'A' and (resid 186 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 210 )
4X-RAY DIFFRACTION4chain 'B' and (resid 163 through 170 )
5X-RAY DIFFRACTION5chain 'B' and (resid 171 through 185 )
6X-RAY DIFFRACTION6chain 'B' and (resid 186 through 201 )
7X-RAY DIFFRACTION7chain 'B' and (resid 202 through 210 )
8X-RAY DIFFRACTION8chain 'C' and (resid 166 through 170 )
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 185 )
10X-RAY DIFFRACTION10chain 'C' and (resid 186 through 201 )
11X-RAY DIFFRACTION11chain 'C' and (resid 202 through 210 )

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