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- PDB-7y1p: CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 7y1p
TitleCRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na
ComponentsAxin-1AXIN1
KeywordsSIGNALING PROTEIN / Wint/beta-catenin signaling pathway
Function / homology
Function and homology information


armadillo repeat domain binding / head development / cell development / dorsal/ventral axis specification / axial mesoderm formation / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei ...armadillo repeat domain binding / head development / cell development / dorsal/ventral axis specification / axial mesoderm formation / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / I-SMAD binding / negative regulation of protein metabolic process / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / negative regulation of fat cell differentiation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / activation of protein kinase activity / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / lateral plasma membrane / signaling adaptor activity / cytoplasmic microtubule organization / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / cell periphery / Degradation of AXIN / sensory perception of sound / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / beta-catenin binding / protein polyubiquitination / positive regulation of protein catabolic process / : / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of peptidyl-serine phosphorylation / cell cortex / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / in utero embryonic development / molecular adaptor activity / Ub-specific processing proteases / positive regulation of protein phosphorylation / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / nucleolus / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsHe, Z. / Yuchi, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022073 China
National Natural Science Foundation of China (NSFC)31972287 China
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na
Authors: He, Z. / Yuchi, Z.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Axin-1
B: Axin-1
C: Axin-1
D: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4555
Polymers67,1764
Non-polymers2781
Water0
1
A: Axin-1


Theoretical massNumber of molelcules
Total (without water)16,7941
Polymers16,7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0722
Polymers16,7941
Non-polymers2781
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Axin-1


Theoretical massNumber of molelcules
Total (without water)16,7941
Polymers16,7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Axin-1


Theoretical massNumber of molelcules
Total (without water)16,7941
Polymers16,7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.343, 155.343, 107.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 114 through 139 or (resid 140...
21(chain B and (resid 114 through 139 or (resid 140...
31(chain C and (resid 114 through 139 or (resid 140...
41(chain D and (resid 114 through 143 or (resid 144...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYS(chain A and (resid 114 through 139 or (resid 140...AA114 - 13941 - 66
12LEULEULEULEU(chain A and (resid 114 through 139 or (resid 140...AA14067
13SERSERSERSER(chain A and (resid 114 through 139 or (resid 140...AA77 - 2154 - 142
14SERSERSERSER(chain A and (resid 114 through 139 or (resid 140...AA77 - 2154 - 142
15SERSERSERSER(chain A and (resid 114 through 139 or (resid 140...AA77 - 2154 - 142
16SERSERSERSER(chain A and (resid 114 through 139 or (resid 140...AA77 - 2154 - 142
21LEULEULYSLYS(chain B and (resid 114 through 139 or (resid 140...BB114 - 13941 - 66
22LEULEULEULEU(chain B and (resid 114 through 139 or (resid 140...BB14067
23SERSERSERSER(chain B and (resid 114 through 139 or (resid 140...BB77 - 2154 - 142
24SERSERSERSER(chain B and (resid 114 through 139 or (resid 140...BB77 - 2154 - 142
25SERSERSERSER(chain B and (resid 114 through 139 or (resid 140...BB77 - 2154 - 142
26SERSERSERSER(chain B and (resid 114 through 139 or (resid 140...BB77 - 2154 - 142
31LEULEULYSLYS(chain C and (resid 114 through 139 or (resid 140...CC114 - 13941 - 66
32LEULEULEULEU(chain C and (resid 114 through 139 or (resid 140...CC14067
33SERSERSERSER(chain C and (resid 114 through 139 or (resid 140...CC77 - 2154 - 142
34SERSERSERSER(chain C and (resid 114 through 139 or (resid 140...CC77 - 2154 - 142
35SERSERSERSER(chain C and (resid 114 through 139 or (resid 140...CC77 - 2154 - 142
36SERSERSERSER(chain C and (resid 114 through 139 or (resid 140...CC77 - 2154 - 142
41LEULEUALAALA(chain D and (resid 114 through 143 or (resid 144...DD114 - 14341 - 70
42ILEILEILEILE(chain D and (resid 114 through 143 or (resid 144...DD14471
43SERSERSERSER(chain D and (resid 114 through 143 or (resid 144...DD77 - 2154 - 142
44SERSERSERSER(chain D and (resid 114 through 143 or (resid 144...DD77 - 2154 - 142
45SERSERSERSER(chain D and (resid 114 through 143 or (resid 144...DD77 - 2154 - 142
46SERSERSERSER(chain D and (resid 114 through 143 or (resid 144...DD77 - 2154 - 142

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Components

#1: Protein
Axin-1 / AXIN1 / Axis inhibition protein 1 / hAxin


Mass: 16794.104 Da / Num. of mol.: 4 / Fragment: RGS-homologous domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli (E. coli) / References: UniProt: O15169
#2: Chemical ChemComp-I5L / (2~{Z},4~{Z})-2-methyl-5-(8-oxidanyldibenzofuran-4-yl)penta-2,4-dienal


Mass: 278.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.81 Å3/Da / Density % sol: 74.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 39114 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 0.584 / Net I/σ(I): 4.7 / Num. measured all: 265978
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.80.89519500.7680.3690.9690.447100
2.64-2.696.70.70719570.8410.2940.7670.458100
2.69-2.746.60.6219290.8330.2580.6720.44999.9
2.74-2.860.51519210.8460.2290.5650.456100
2.8-2.866.50.44419720.9290.1890.4830.459100
2.86-2.937.10.40219440.9350.1610.4330.467100
2.93-37.10.34219610.9530.1380.3690.47100
3-3.087.10.29819210.9650.120.3220.489100
3.08-3.1770.23619500.9780.0960.2550.496100
3.17-3.2870.18119430.9840.0740.1960.539100
3.28-3.396.90.14319920.9940.0590.1550.582100
3.39-3.536.80.11919440.9910.0490.1290.694100
3.53-3.696.10.09319540.9950.0410.1020.71699.9
3.69-3.887.10.08519430.9950.0340.0920.733100
3.88-4.137.20.07819530.9960.0310.0840.788100
4.13-4.457.10.06719600.9960.0270.0720.798100
4.45-4.8970.06119660.9970.0250.0660.76399.9
4.89-5.66.20.05619630.9960.0240.0610.66499.9
5.6-7.057.20.05519680.9970.0220.0590.56799.9
7.05-506.50.03820230.9990.0160.0420.61399.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dk8

1dk8


Resolution: 2.602→38.836 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1996 5.11 %
Rwork0.2079 37034 -
obs0.2089 39030 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.99 Å2 / Biso mean: 54.5658 Å2 / Biso min: 23.36 Å2
Refinement stepCycle: final / Resolution: 2.602→38.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 21 0 4383
Biso mean--82.4 --
Num. residues----556
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1676X-RAY DIFFRACTION5.695TORSIONAL
12B1676X-RAY DIFFRACTION5.695TORSIONAL
13C1676X-RAY DIFFRACTION5.695TORSIONAL
14D1676X-RAY DIFFRACTION5.695TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.602-2.66680.29081460.27782667100
2.6668-2.73890.28791400.25682614100
2.7389-2.81940.26211440.25582639100
2.8194-2.91040.31261420.25292638100
2.9104-3.01440.28371410.26142614100
3.0144-3.1350.30771460.25882671100
3.135-3.27770.27541420.23622601100
3.2777-3.45040.27321410.2312675100
3.4504-3.66640.24271420.21232648100
3.6664-3.94920.20261420.1962645100
3.9492-4.34620.22071420.18612656100
4.3462-4.9740.18681440.17112655100
4.974-6.26240.19221420.20642668100
6.2624-38.8360.17091420.1671264397

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