[English] 日本語
Yorodumi
- PDB-7y1p: CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / axial mesoderm formation / dorsal/ventral axis specification / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex ...beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / axial mesoderm formation / dorsal/ventral axis specification / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of protein metabolic process / nucleocytoplasmic transport / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / lateral plasma membrane / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / cytoplasmic microtubule organization / signaling adaptor activity / protein serine/threonine kinase binding / protein serine/threonine kinase activator activity / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / Degradation of AXIN / sensory perception of sound / 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 / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / protein-containing complex assembly / cytoplasmic vesicle / cell cortex / molecular adaptor activity / Estrogen-dependent gene expression / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein
Axin-1 / 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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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