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- PDB-6zt0: Crystal structure of the Eiger TNF domain/Grindelwald extracellul... -

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Basic information

Entry
Database: PDB / ID: 6zt0
TitleCrystal structure of the Eiger TNF domain/Grindelwald extracellular domain complex
Components
  • Protein eiger
  • Protein grindelwald
KeywordsSIGNALING PROTEIN / TNF receptor / JNK cascade / TNF / signaling / extracellular / tumor necrosis factor
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / response to tumor cell / positive regulation of sensory perception of pain / negative regulation of neuromuscular synaptic transmission / melanization defense response / asymmetric protein localization involved in cell fate determination / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / engulfment of apoptotic cell / tumor necrosis factor receptor binding ...HuR (ELAVL1) binds and stabilizes mRNA / response to tumor cell / positive regulation of sensory perception of pain / negative regulation of neuromuscular synaptic transmission / melanization defense response / asymmetric protein localization involved in cell fate determination / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / engulfment of apoptotic cell / tumor necrosis factor receptor binding / positive regulation of programmed cell death / apical protein localization / negative regulation of multicellular organism growth / glial cell proliferation / negative regulation of reactive oxygen species biosynthetic process / cellular response to amino acid starvation / cytokine activity / tumor necrosis factor-mediated signaling pathway / positive regulation of JNK cascade / wound healing / neuron cellular homeostasis / positive regulation of reactive oxygen species metabolic process / defense response to Gram-negative bacterium / immune response / positive regulation of cell migration / apical plasma membrane / positive regulation of apoptotic process / receptor ligand activity / signaling receptor binding / innate immune response / apoptotic process / extracellular space / plasma membrane
Similarity search - Function
: / 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
Protein eiger / Tumor necrosis factor receptor superfamily member grnd
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPalmerini, V. / Cecatiello, V. / Pasqualato, S. / Mapelli, M.
CitationJournal: Nat Commun / Year: 2021
Title: Drosophila TNFRs Grindelwald and Wengen bind Eiger with different affinities and promote distinct cellular functions.
Authors: Palmerini, V. / Monzani, S. / Laurichesse, Q. / Loudhaief, R. / Mari, S. / Cecatiello, V. / Olieric, V. / Pasqualato, S. / Colombani, J. / Andersen, D.S. / Mapelli, M.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Protein eiger
AAAA: Protein grindelwald
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6525
Polymers22,4662
Non-polymers1863
Water2,126118
1
A: Protein eiger
AAAA: Protein grindelwald
hetero molecules

A: Protein eiger
AAAA: Protein grindelwald
hetero molecules

A: Protein eiger
AAAA: Protein grindelwald
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95615
Polymers67,3986
Non-polymers5599
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)78.707, 78.707, 57.657
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-671-

HOH

31A-681-

HOH

41A-684-

HOH

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Components

#1: Protein Protein eiger


Mass: 16546.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: egr, Darth, CG12919 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MUJ1
#2: Protein Protein grindelwald


Mass: 5919.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: grnd, CG10176 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VJ83
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5 14 % PEG 4000 0.2 M MgCl2 concentration 28 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.02→57.66 Å / Num. obs: 13860 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 27.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.207 / Net I/σ(I): 8.6
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 663 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
autoPROCdata collection
PHENIX1.17_3644refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RJ8

1rj8


Resolution: 2.02→44.02 Å / SU ML: 0.2682 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 25.5697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 619 4.47 %
Rwork0.1913 13236 -
obs0.1925 13855 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.29 Å2
Refinement stepCycle: LAST / Resolution: 2.02→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 12 118 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271604
X-RAY DIFFRACTIONf_angle_d0.58192167
X-RAY DIFFRACTIONf_chiral_restr0.0463222
X-RAY DIFFRACTIONf_plane_restr0.004292
X-RAY DIFFRACTIONf_dihedral_angle_d21.7828221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.220.30171680.27633220X-RAY DIFFRACTION99.71
2.22-2.540.23961710.22813256X-RAY DIFFRACTION100
2.55-3.210.23051260.19623333X-RAY DIFFRACTION100
3.21-44.020.18241540.15933427X-RAY DIFFRACTION99.92
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)
14.02188116307-0.160300763574-0.9575768329553.759108379221.052020846385.74252002090.133339275173-0.2697953640170.1428189285560.4046551863210.137422671725-0.3704683503810.1963677563550.2096893851740.08778946413790.236708254362-0.0330483889662-0.132954970150.243555299219-0.04519713445850.294281849551-23.930155628128.159974648516.9939618157
22.82311602429-0.6702608164830.9354679756283.263224082331.76808807285.10115254308-0.469702873458-0.315838277017-1.012936483480.399203606706-0.255460270422-0.6911867116811.136045351521.008947704260.2339847991580.4269622276220.100263591310.1382771045510.464626174773-0.02295037419090.763668357455-16.450103588513.73712946225.03084741666
31.97983638222-0.881874886236-1.964206670748.974767274046.447836098145.026627454870.110212855568-0.06764666618640.2232562674480.1870674369710.0495240296374-0.248715340171-0.153269671130.464077900553-0.1323010584930.2649048089370.00518074292042-0.09269434807840.278635224942-0.02557722426810.39015477913-23.496283202731.067864448415.9587344386
42.192353908-0.2776586929190.04600556617422.50662656087-1.070800220143.51747156180.014882779441-0.5294049486310.015011943510.481312574053-0.0962839449585-0.414960787694-0.1016348293360.4100999114120.05070531650170.255916114122-0.0123941439698-0.06250004474680.2726796246420.002402601734670.279359957851-25.126764046922.424849520320.041688923
52.754372155640.1451284841980.739700357752.14494754306-1.174202976392.823465746830.0538552200492-0.0269853886243-0.02136615121790.08848254080360.114588531753-0.117983223241-0.03624348726620.210448617612-0.1479939421420.210308588316-0.001034283696340.02208461161250.175355234147-0.04418402060120.32296980518-26.984600794118.59366057172.05409148415
61.534044776810.3418953692022.925987086560.06567499904740.1613590791959.85432648089-0.208752871611-0.100496244955-0.05772723557450.0248254403368-0.0259067242585-0.364066632997-0.0710245440147-0.1487651646910.2818178646770.213842512570.003876320117770.004397870086230.1484909349270.0202840588250.254152428559-31.318232891714.66091372826.05886265928
70.727186484039-1.20262775902-1.197349056722.28388803412.611065764123.068981603790.2959929233410.6460822572680.698396534611-0.9208717563050.304104372613-1.08442895477-1.09583766767-0.260483781427-0.6787988536410.4205180476180.04947975105080.1193624034360.3748015816230.04926271505240.183676646916-33.436421095627.5250906341-11.0630565391
82.132971825010.746515973938-0.3902964203882.56239205807-0.2522662432881.895237358250.116659817185-0.255041123847-0.1103761687460.2819386081730.04692463143740.009859212422350.1946732928360.2567032529280.04636087775470.1999029796070.0238337038618-0.05944514940940.192894377926-0.002148478896390.2018632764-33.379694385819.031761488112.4848348658
92.412296189970.4724494998840.3016207107242.86706339751-0.6747971103892.187833268910.0582030779622-0.239730732103-0.2635524505550.5355559009810.12570815882-0.424092305698-0.2649023482520.418619036357-0.1192308174440.23924615720.0385827561032-0.08447361890550.2306780806880.03911369756610.386896545293-21.742994636916.412086305712.5957637627
104.602792262-1.08760124271-0.6979659741237.115103463870.2091894284353.524196831790.0645461845791-0.005893041308740.66506315109-0.2320802932220.189707096013-0.657827995044-0.4051927067180.269879467781-0.141848502450.161624195331-0.05048054897270.004161237924620.1811496220880.01233992430530.260738282265-26.119756392832.28549201314.36215360042
114.688394611610.490445874845-1.978449973542.292283730511.627971435982.37948856764-0.234250101459-0.345072086372-0.3776145895910.492138076174-0.369804325277-0.210042559992-0.09243001536650.05428563782290.5661517923770.22333453011-0.0243007527665-0.0200240622570.272582125753-0.02069642250310.182891541917-31.544005650523.789973687919.7486362911
124.54986336546-2.646060956721.166061990872.0008217656-0.8520529197950.471485239035-0.03179318263290.144991529052-0.0391101268916-0.487934086513-0.201334387132-0.9646734232830.3615402075340.6695673186110.0163649479140.3203237272610.01449339228930.1160461342010.300156595329-0.04466226358570.479635012212-24.2058298869-0.0434166939275-9.87994688415
133.62818083738-0.411947715363-1.405011933053.161264202611.631902483395.92748023109-0.03992909057970.257396612444-0.165366621073-0.197622217506-0.08115792565180.02567206523060.0480605703577-0.02871031387250.03682873520750.203652466191-0.008379473237110.01252357950360.2367280679110.01767482908050.3539601497-26.48843437669.55144361444-9.78371530543
142.42628428245-3.22643181421-0.6825931946868.426629349965.481645762615.2362228380.559374349721-0.03179145845920.489920820432-1.34557436067-0.422980106272-0.709683475052-0.8281629646430.245584963464-0.2183992664550.425133271012-0.02582379904590.1235236832680.279954784652-0.004308667287310.380785195685-22.856669600520.4911281321-15.8416379979
159.66346384195-1.41646575453-2.618533280826.89476726934-0.9331883717487.07739788937-0.19584397045-0.349993949855-0.584124446495-0.3843195366020.106223474068-1.15788126670.2238487183650.3127147762520.04537929207120.265300269085-0.04929153715580.1399326148770.44562653133-0.008450258151220.557464696657-16.705129261111.2040798615-11.4867717342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 275 through 288 )
2X-RAY DIFFRACTION2chain 'A' and (resid 289 through 299 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 309 )
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 338 )
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 353 )
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 362 )
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 371 )
8X-RAY DIFFRACTION8chain 'A' and (resid 372 through 382 )
9X-RAY DIFFRACTION9chain 'A' and (resid 383 through 396 )
10X-RAY DIFFRACTION10chain 'A' and (resid 397 through 408 )
11X-RAY DIFFRACTION11chain 'A' and (resid 409 through 415 )
12X-RAY DIFFRACTION12chain 'G' and (resid 31 through 44 )
13X-RAY DIFFRACTION13chain 'G' and (resid 45 through 61 )
14X-RAY DIFFRACTION14chain 'G' and (resid 62 through 69 )
15X-RAY DIFFRACTION15chain 'G' and (resid 70 through 81 )

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