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- PDB-8slr: Crystal Structure of mouse TRAIL -

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Basic information

Entry
Database: PDB / ID: 8slr
TitleCrystal Structure of mouse TRAIL
ComponentsTumor necrosis factor ligand superfamily member 10
KeywordsCYTOKINE / TRAIL / APOPTOSIS / PRO-APOPTOTIC / TNF SUPERFAMILY
Function / homology
Function and homology information


TRAIL signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TRAIL binding / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / cytokine activity ...TRAIL signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TRAIL binding / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / cytokine activity / response to insulin / male gonad development / positive regulation of canonical NF-kappaB signal transduction / immune response / positive regulation of apoptotic process / apoptotic process / extracellular space / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Tumour necrosis factor ligand 10/11 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tumor necrosis factor ligand superfamily member 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPedersen, L.C. / Xu, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC-ES102645 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR070179 United States
CitationJournal: Elife / Year: 2024
Title: Heparan sulfate promotes TRAIL-induced tumor cell apoptosis.
Authors: Luo, Y. / Hao, H. / Wang, Z. / Ong, C.Y. / Dutcher, R. / Xu, Y. / Liu, J. / Pedersen, L.C. / Xu, D.
History
DepositionApr 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 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
D: Tumor necrosis factor ligand superfamily member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5647
Polymers20,2241
Non-polymers3406
Water1,856103
1
D: Tumor necrosis factor ligand superfamily member 10
hetero molecules

D: Tumor necrosis factor ligand superfamily member 10
hetero molecules

D: Tumor necrosis factor ligand superfamily member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,69221
Polymers60,6723
Non-polymers1,02018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15660 Å2
ΔGint-186 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.350, 147.350, 147.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11D-301-

ZN

21D-302-

CL

31D-467-

HOH

41D-482-

HOH

51D-503-

HOH

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Components

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Protein , 1 types, 1 molecules D

#1: Protein Tumor necrosis factor ligand superfamily member 10 / TNF-related apoptosis-inducing ligand / Protein TRAIL


Mass: 20223.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf10, Trail / Production host: Escherichia coli (E. coli) / Strain (production host): Origami-B / References: UniProt: P50592

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.59 Å3/Da / Density % sol: 81.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein: 4.4mg/ml Trail+ 1mM 12merNS2S6S in 25mM HEPES pH 7.1, 150mM NaCl Reservoir: 0.085M HEPES pH 7.5, 8.5% PEG 8000, 8.5%EG

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22033 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 40.51 Å2 / CC1/2: 0.994 / CC star: 0.998 / Net I/σ(I): 4.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1097 / CC1/2: 0.784 / CC star: 0.937 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DU3

1du3


Resolution: 2.4→44.43 Å / SU ML: 0.1919 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1825 1089 4.99 %
Rwork0.1598 20722 -
obs0.1609 21811 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 15 103 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611358
X-RAY DIFFRACTIONf_angle_d0.81631837
X-RAY DIFFRACTIONf_chiral_restr0.0566193
X-RAY DIFFRACTIONf_plane_restr0.0076238
X-RAY DIFFRACTIONf_dihedral_angle_d14.6437498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.24391330.23232518X-RAY DIFFRACTION98.29
2.51-2.640.21661300.19592512X-RAY DIFFRACTION98.51
2.64-2.810.18421350.18222523X-RAY DIFFRACTION98.85
2.81-3.020.18661360.18752564X-RAY DIFFRACTION99.08
3.02-3.330.17711330.15952557X-RAY DIFFRACTION99.23
3.33-3.810.17251360.15172606X-RAY DIFFRACTION99.89
3.81-4.80.1421400.11872645X-RAY DIFFRACTION99.79
4.8-44.430.21491460.16852797X-RAY DIFFRACTION99.16
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)
12.9442262318-0.6871754126583.339231247556.11383842557-0.1852308598689.512437393760.4174989487650.4810514303030.4946642289930.346924602259-0.182524253870.106241619497-0.1012917604120.4315298686190.2358288513470.366303736758-0.002230616586770.09469322302280.222672210856-0.003872452828450.312735755422.068208839428.35568000939.89880976035
24.20355470658-2.24105252099-1.011593104091.44048963713-0.5260941113855.081864577580.236875290587-1.228740140270.9461399143490.132560137770.04656605677250.7106414502191.715722576320.374651550784-0.3621931255481.214165993780.00292525279885-0.2896358250660.860926026234-0.06372943126781.039711382753.7703353977625.2241858302-2.39792374384
36.29672848999-5.31994742245.608029388145.05717971713-3.916664541516.248412472570.3806704576750.564137754099-0.322795043547-1.23627788476-0.193670352642-0.3823665723630.1944713076690.435903399515-0.3367590750680.5480008357480.08762145325890.02136064593630.444707425755-0.0447898062590.392360468895-4.1680670381929.34989711936.2758051582
48.77034532274-2.916594306265.235024483023.54518173771-1.693609617633.1579173432-0.46521179815-0.780775595058-0.5937336874130.613816094970.5975993186760.584396153617-0.454566479569-0.576567501151-0.2528127382310.3747793836180.05465866552080.07656464677960.5111353396710.06831775181250.4118904157630.48376637375519.8218475227.3812567607
51.719661700490.174804945108-0.2599067010892.281310305760.9114266202651.485161771770.0174717998697-0.2234091418010.03935559680370.170690380103-0.004641205881940.0678626138191-0.112530613776-0.0528455660027-0.01564970941810.2818524069380.0366392239664-0.03126862688970.353194653360.0264844902480.249872106337.1691122640323.069231451923.4409096637
61.435671748480.154442275671-0.06833164175354.973071347231.246173601872.487916611620.02193797006450.222140780278-0.116466074766-0.1666734866240.009213601789190.05982423179960.135408355576-0.133801732114-0.02402460405320.3138184541690.0319452868982-0.01544944721630.386591726233-0.003389032606880.3137686379062.31415579822.73683934158.88408942754
71.29769626573-0.3395164077060.3414979301381.922295714420.7292537917381.76484042575-0.003913520205760.0871955401213-0.247854456808-0.2161030949160.03035386195330.2367476029230.152179104583-0.26731274963-0.1298911955240.342839412054-0.00782470681322-0.02144317728640.385067265245-0.00551298509780.3612937441583.7232802379910.92936436099.55595479507
86.462523467244.174128695744.077646251413.831683921544.098322053844.89587512580.027482309317-0.02852326318380.06738979079560.02075002216280.07228419089150.0364604098705-0.104843867087-0.0194245868841-0.07690750409060.2473004649420.04560871825430.0006827770420620.2704027575850.01034101931330.1980825435994.5593832364731.197957734119.0438617394
97.382020767991.127250405994.716265199391.716612988280.04144755870423.357847683510.124261989051-0.865080233403-0.1586125533670.129975974598-0.04894184865880.03760994859750.10349238253-1.07641826488-0.123412872450.331147286129-0.01990938997650.00499150079780.4765601032960.02917597435080.47017510807-2.4054596261712.305767809218.7122942154
103.090068559680.233518070869-1.392044628712.240399229-0.5826925103146.834118304710.346454662809-0.3674407090590.1060408902980.371593619678-0.1851432114-0.430221783997-0.1021640031420.685808077274-0.20931753860.2810831849870.0563206393365-0.04394633482440.301703399267-0.05159283818570.2995980509814.578948943423.806079466622.6194302851
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: D / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'D' and (resid 124 through 133 )124 - 1331 - 10
22chain 'D' and (resid 134 through 143 )134 - 14311 - 20
33chain 'D' and (resid 144 through 153 )144 - 15321 - 30
44chain 'D' and (resid 154 through 163 )154 - 16331 - 40
55chain 'D' and (resid 164 through 197 )164 - 19741 - 74
66chain 'D' and (resid 198 through 232 )198 - 23275 - 102
77chain 'D' and (resid 233 through 254 )233 - 254103 - 124
88chain 'D' and (resid 255 through 264 )255 - 264125 - 134
99chain 'D' and (resid 265 through 277 )265 - 277135 - 147
1010chain 'D' and (resid 278 through 285 )278 - 285148 - 155

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