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- PDB-7x9g: Crystal structure of human EDA and EDAR -

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Basic information

Entry
Database: PDB / ID: 7x9g
TitleCrystal structure of human EDA and EDAR
Components
  • Ectodysplasin-A, secreted form
  • Tumor necrosis factor receptor superfamily member EDAR
KeywordsMEMBRANE PROTEIN / ligand-receptor complex
Function / homology
Function and homology information


trachea gland development / animal organ development / salivary gland cavitation / regulation of non-canonical NF-kappaB signal transduction / death receptor agonist activity / TNFs bind their physiological receptors / collagen trimer / tumor necrosis factor receptor binding / death receptor binding / pigmentation ...trachea gland development / animal organ development / salivary gland cavitation / regulation of non-canonical NF-kappaB signal transduction / death receptor agonist activity / TNFs bind their physiological receptors / collagen trimer / tumor necrosis factor receptor binding / death receptor binding / pigmentation / odontogenesis of dentin-containing tooth / hair follicle placode formation / hair follicle development / epidermis development / canonical Wnt signaling pathway / lipid droplet / cell-matrix adhesion / positive regulation of JNK cascade / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / apical part of cell / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / gene expression / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / cytoskeleton / immune response / intracellular membrane-bounded organelle / signaling receptor binding / apoptotic process / positive regulation of gene expression / endoplasmic reticulum membrane / extracellular space / membrane / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor EDAR, N-terminal / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Ectodysplasin-A / Tumor necrosis factor receptor superfamily member EDAR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYu, K. / Wan, F. / Huang, C. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants.
Authors: Yu, K. / Huang, C. / Wan, F. / Jiang, C. / Chen, J. / Li, X. / Wang, F. / Wu, J. / Lei, M. / Wu, Y.
History
DepositionMar 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ectodysplasin-A, secreted form
B: Ectodysplasin-A, secreted form
C: Tumor necrosis factor receptor superfamily member EDAR


Theoretical massNumber of molelcules
Total (without water)48,5873
Polymers48,5873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.169, 87.169, 156.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ectodysplasin-A, secreted form


Mass: 17470.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDA, ED1, EDA2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92838
#2: Protein Tumor necrosis factor receptor superfamily member EDAR / Anhidrotic ectodysplasin receptor 1 / Downless homolog / EDA-A1 receptor / Ectodermal dysplasia ...Anhidrotic ectodysplasin receptor 1 / Downless homolog / EDA-A1 receptor / Ectodermal dysplasia receptor / Ectodysplasin-A receptor


Mass: 13645.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDAR, DL / Cell line (production host): High Five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNE0

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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: 2.35 Å3/Da / Density % sol: 47.72 % / Mosaicity: 0.457 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine, pH9.0, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10861 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.85 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Χ2: 0.891 / Net I/σ(I): 11.4 / Num. measured all: 37897
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.93.40.69611230.6330.4370.8240.95499.8
2.9-3.023.60.45510650.8320.2790.5350.96799.8
3.02-3.153.50.27710670.9170.1710.3270.97599.6
3.15-3.323.50.16510890.9630.1040.1950.95199.7
3.32-3.533.30.10310810.9790.0670.1240.98299.8
3.53-3.83.60.06410930.9910.0390.0760.91499.8
3.8-4.183.60.04710910.9950.0290.0550.88899.7
4.18-4.793.40.03710750.9950.0240.0450.80199.9
4.79-6.033.60.03610900.9960.0220.0420.71699.9
6.03-503.40.03410870.9970.0210.0410.76399.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RJ7

1rj7


Resolution: 2.8→34.71 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 30.58 / Stereochemistry target values: MLHL / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflection
Rfree0.282 407 4.11 %
Rwork0.248 9485 -
obs0.2493 9892 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.52 Å2 / Biso mean: 53.1004 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 2.8→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 0 0 2853
Num. residues----367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.210.40581020.29672567266973
3.21-4.040.31750.25534263601100
4.04-34.710.22661300.228234923622100
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)
10.1016-0.0544-0.04020.07040.04730.0345-0.0526-0.0818-0.05930.21560.07890.0007-0.1007-0.0234-0.02590.2208-0.0257-0.0580.19080.1720.1046-39.806513.6707-22.1209
20.0509-0.04640.04080.043-0.03590.031-0.0120.0136-0.0258-0.05210.0250.05540.09650.04640.06710.68660.0321-0.00550.5954-0.35550.5939-43.38983.7561-42.0308
30.2561-0.07680.04230.17130.21930.3947-0.041-0.2633-0.38790.1475-0.2103-0.16520.25760.1006-0.30260.3134-0.09130.08810.21350.26560.2386-44.02686.3398-25.2308
40.06710.0279-0.01790.0266-0.02260.01920.0207-0.0408-0.03170.0771-0.02260.08920.0106-0.05770.09690.4052-0.0380.2860.41130.20310.4635-50.16595.7446-22.1916
50.0944-0.015-0.00980.0361-0.02420.02720.0030.0981-0.1408-0.071-0.02730.02760.04590.0199-0.06670.3220.03580.07570.2730.0149-0.2302-45.138215.7858-34.9519
60.0452-0.10970.03770.3141-0.0620.04230.09050.1681-0.1309-0.2592-0.0610.1498-0.0324-0.0637-0.08290.3420.0121-0.07770.3735-0.02820.1103-53.53516.0542-37.94
70.0081-0.0130.01010.0257-0.01840.0121-0.03050.0154-0.0163-0.0395-0.02120.0131-0.0223-0.0402-0.06330.8462-0.12680.21610.7698-0.22510.2118-41.478916.8658-51.687
80.01190.0110.00090.0323-0.00580.04090.0002-0.0033-0.0212-0.04030.0518-0.008-0.0222-0.00420.11760.341-0.02830.31320.1361-0.07010.0492-48.240620.277-29.8326
90.0251-0.0054-0.02180.0096-0.00210.0454-0.04240.0463-0.2068-0.12510.0135-0.0162-0.01050.0570.13390.2164-0.1090.34010.1616-0.19950.0682-47.340810.1753-33.9961
100.0241-0.06820.02320.3835-0.09130.0464-0.0029-0.2144-0.01590.26870.070.1818-0.1057-0.1738-0.11890.1116-0.12450.1560.12460.3047-0.1494-48.507118.1208-18.2593
110.0282-0.01020.03160.3379-0.00590.0661-0.0241-0.64690.4270.31080.13280.3603-0.09280.04250.35280.43260.06910.44170.7971-0.19930.8438-18.0083.9024-10.9405
120.36750.233-0.07640.9193-0.20660.5680.0276-0.00060.3573-0.16960.05960.4535-0.09130.05090.2935-0.0161-0.0198-0.00520.11270.01030.3407-8.29736.3835-23.2305
130.1463-0.0278-0.01070.43140.23590.12850.1143-0.32690.36910.1561-0.00580.0887-0.02210.10250.0070.10960.02780.17070.3101-0.27810.4823-8.85879.0972-11.6894
140.15330.0423-0.02890.2269-0.04290.0195-0.058-0.07810.16330.1982-0.08730.4224-0.20450.0277-0.01740.25-0.0164-0.00880.30810.01480.6266-10.81962.816-15.0357
150.1907-0.19480.09260.5721-0.13620.0484-0.0111-0.1124-0.3160.39470.0529-0.18560.00710.02840.12790.3847-0.0736-0.15950.2650.25430.6803-31.7247-2.7506-19.7953
160.09540.0429-0.08850.2642-0.26030.26890.11540.114-0.00030.09270.12920.10290.10380.17640.20450.9231-0.1417-0.41920.9374-0.35261.1562-22.222-12.374-35.5825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 255 )A247 - 255
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 265 )A256 - 265
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 287 )A266 - 287
4X-RAY DIFFRACTION4chain 'A' and (resid 288 through 298 )A288 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 313 )A299 - 313
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 335 )A314 - 335
7X-RAY DIFFRACTION7chain 'A' and (resid 336 through 343 )A336 - 343
8X-RAY DIFFRACTION8chain 'A' and (resid 344 through 354 )A344 - 354
9X-RAY DIFFRACTION9chain 'A' and (resid 355 through 378 )A355 - 378
10X-RAY DIFFRACTION10chain 'A' and (resid 379 through 390 )A379 - 390
11X-RAY DIFFRACTION11chain 'B' and (resid 247 through 298 )B247 - 298
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 343 )B299 - 343
13X-RAY DIFFRACTION13chain 'B' and (resid 344 through 364 )B344 - 364
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 389 )B365 - 389
15X-RAY DIFFRACTION15chain 'C' and (resid 44 through 101 )C44 - 101
16X-RAY DIFFRACTION16chain 'C' and (resid 102 through 137 )C102 - 137

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