[English] 日本語
Yorodumi
- PDB-1rj7: Crystal structure of EDA-A1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rj7
TitleCrystal structure of EDA-A1
ComponentsEctodysplasin A
KeywordsHORMONE/GROWTH FACTOR / EDA / TNF / beta-bulge / morphogen / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


trachea gland development / animal organ development / salivary gland cavitation / regulation of non-canonical NF-kappaB signal transduction / TNFs bind their physiological receptors / death receptor agonist activity / 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 / TNFs bind their physiological receptors / death receptor agonist activity / collagen trimer / tumor necrosis factor receptor binding / death receptor binding / pigmentation / odontogenesis of dentin-containing tooth / hair follicle placode formation / canonical Wnt signaling pathway / lipid droplet / cell-matrix adhesion / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / apical part of cell / gene expression / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / cytoskeleton / immune response / signaling receptor binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / positive regulation of gene expression / extracellular space / membrane / plasma membrane
Similarity search - Function
TNF family profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHymowitz, S.G. / Compaan, D.M. / Yan, M. / Ackerly, H. / Dixit, V.M. / Starovasnik, M.A. / de Vos, A.M.
CitationJournal: Structure / Year: 2003
Title: The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
Authors: Hymowitz, S.G. / Compaan, D.M. / Yan, M. / Wallweber, H.J. / Dixit, V.M. / Starovasnik, M.A. / de Vos, A.M.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 19, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectodysplasin A
B: Ectodysplasin A
D: Ectodysplasin A
E: Ectodysplasin A
F: Ectodysplasin A
G: Ectodysplasin A
H: Ectodysplasin A
I: Ectodysplasin A
J: Ectodysplasin A
K: Ectodysplasin A
L: Ectodysplasin A
M: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)214,61212
Polymers214,61212
Non-polymers00
Water6,107339
1
A: Ectodysplasin A
B: Ectodysplasin A
D: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-24 kcal/mol
Surface area16810 Å2
MethodPISA
2
E: Ectodysplasin A
F: Ectodysplasin A
G: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-26 kcal/mol
Surface area17400 Å2
MethodPISA
3
H: Ectodysplasin A
I: Ectodysplasin A
J: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-22 kcal/mol
Surface area17000 Å2
MethodPISA
4
K: Ectodysplasin A
L: Ectodysplasin A
M: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-24 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.657, 279.687, 54.175
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit is composed of 4 trimers. A trimer is the biologically relevant unit

-
Components

#1: Protein
Ectodysplasin A / Ectodermal dysplasia protein / EDA protein


Mass: 17884.293 Da / Num. of mol.: 12 / Fragment: TNF domain of EDA-A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ED1, EDA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92838
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M di-sodium hydrogen phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5 mg/mlprotein1drop
220 %PEG33501reservoir
30.2 Mdi-sodium hydrogen phosphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 70270 / Num. obs: 66402 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Num. unique all: 6606 / Rsym value: 0.24 / % possible all: 94.5
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 66596 / % possible obs: 94.4 % / Num. measured all: 215586
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.239

-
Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated model of Apo2L/TRAIL from 1d0g

1d0g


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.162 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.926 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26029 7099 10.7 %THIN SHELLS
Rwork0.19424 ---
all0.2012 59179 --
obs0.20127 59179 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.1 Å2
2---0.24 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 0 0 339 13887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213834
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212449
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93818751
X-RAY DIFFRACTIONr_angle_other_deg0.794328980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99851719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29624.253609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.827152335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2761561
X-RAY DIFFRACTIONr_chiral_restr0.0780.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022817
X-RAY DIFFRACTIONr_nbd_refined0.1970.22010
X-RAY DIFFRACTIONr_nbd_other0.2550.214127
X-RAY DIFFRACTIONr_nbtor_other0.0830.27846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2401
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.256
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.2194
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.219
X-RAY DIFFRACTIONr_mcbond_it1.67258579
X-RAY DIFFRACTIONr_mcangle_it2.4613904
X-RAY DIFFRACTIONr_scbond_it2.52165255
X-RAY DIFFRACTIONr_scangle_it3.52384847
LS refinement shellResolution: 2.3→2.348 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.291 520 -
Rwork0.199 3291 -
obs--94.5 %
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)
14.3322-0.32331.81942.177-0.08323.54120.06780.14360.2598-0.0609-0.1406-0.0161-0.20140.09480.07280.114-0.00930.02030.077-0.01340.114420.543513.171570.8606
24.07430.30780.23353.82710.87524.78470.1585-0.1445-0.44860.173-0.14870.26280.2546-0.3195-0.00980.1028-0.03970.00790.12610.01340.24677.9038-5.178475.8746
35.5174-1.12960.8724.5622-0.86444.91230.14440.5165-0.4524-0.2753-0.1485-0.14090.10430.32480.00410.10470.0324-0.02930.1445-0.07640.249728.9338-7.742166.8665
43.6555-0.17351.47851.8233-0.2623.13970.06210.0994-0.3167-0.1462-0.00290.07440.2836-0.0873-0.05920.1140.00590.02680.0531-0.00240.070341.014820.644652.222
53.8813-0.33640.82492.048-0.34631.4303-0.01550.26830.079-0.21020.0022-0.03380.00610.11010.01330.1127-0.00260.03420.08620.02230.016644.194540.016740.7622
63.89690.87320.91372.52980.27182.5887-0.0329-0.24520.10780.13420.00820.2632-0.0616-0.14620.02470.10990.0350.04410.04750.01120.067835.11540.433161.6959
74.25380.4096-0.91164.5235-0.22754.70790.0377-0.36620.27510.2993-0.0437-0.1718-0.18180.38290.00610.1236-0.0413-0.03070.1679-0.03850.18734.7225113.107914.3878
84.7557-0.3344-2.05272.09180.22064.4333-0.0529-0.1783-0.2547-0.1029-0.02220.09170.5380.20350.07510.21320.0241-0.01840.08590.02980.1282-2.803892.02779.9094
92.89770.4164-0.34683.3953-0.44125.37180.10020.1380.4842-0.08240.12120.4505-0.0689-0.7224-0.22140.1305-0.0048-0.03960.18060.05840.293-15.93109.92664.0483
105.6217-1.3003-1.29753.15710.33392.1657-0.00590.3027-0.0871-0.27320.04960.33710.132-0.2145-0.04370.1266-0.0311-0.03990.07710.02280.120311.741164.289416.9696
114.34750.294-1.59211.945-0.55372.96670.0485-0.19220.36970.15890.0176-0.0086-0.2628-0.0333-0.0660.12890.01160.00350.0424-0.01340.150316.971883.291228.6191
123.7683-0.7335-0.21163.1462-0.18452.1651-0.0041-0.3112-0.1380.20820.04810.14330.039-0.1328-0.0440.10260.0110.00150.10530.03550.06821.239262.603737.6252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA247 - 39019 - 162
2X-RAY DIFFRACTION2BB247 - 39019 - 162
3X-RAY DIFFRACTION3DC247 - 39019 - 162
4X-RAY DIFFRACTION4ED242 - 39014 - 162
5X-RAY DIFFRACTION5FE247 - 39019 - 162
6X-RAY DIFFRACTION6GF247 - 39019 - 162
7X-RAY DIFFRACTION7HG247 - 38819 - 160
8X-RAY DIFFRACTION8IH247 - 38919 - 161
9X-RAY DIFFRACTION9JI248 - 39020 - 162
10X-RAY DIFFRACTION10KJ247 - 39119 - 163
11X-RAY DIFFRACTION11LK246 - 39018 - 162
12X-RAY DIFFRACTION12ML247 - 39019 - 162
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 66278 / % reflection Rfree: 10 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.28

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more