[English] 日本語
Yorodumi
- PDB-3t7u: A NeW Crystal structure of APC-ARM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t7u
TitleA NeW Crystal structure of APC-ARM
ComponentsAdenomatous polyposis coli protein
KeywordsCELL ADHESION / Armadillo repeats domain
Function / homology
Function and homology information


APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process ...APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / bicellular tight junction assembly / pattern specification process / negative regulation of microtubule depolymerization / catenin complex / beta-catenin destruction complex / heart valve development / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / regulation of microtubule-based process / microtubule plus-end binding / 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 / protein kinase regulator activity / Wnt signalosome / cell fate specification / Disassembly of the destruction complex and recruitment of AXIN to the membrane / endocardial cushion morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / dynein complex binding / mitotic cytokinesis / bicellular tight junction / lateral plasma membrane / adherens junction / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / kinetochore / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / insulin receptor signaling pathway / cell migration / nervous system development / lamellipodium / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / microtubule binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat ...Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Adenomatous polyposis coli protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsZhang, Z. / Wu, G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of the armadillo repeat domain of adenomatous polyposis coli which reveals its inherent flexibility
Authors: Zhang, Z. / Lin, K. / Gao, L. / Chen, L. / Shi, X. / Wu, G.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenomatous polyposis coli protein
B: Adenomatous polyposis coli protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2874
Polymers84,0972
Non-polymers1902
Water46826
1
A: Adenomatous polyposis coli protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2383
Polymers42,0481
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)42,0481
Polymers42,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.496, 72.496, 129.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 407 - 733 / Label seq-ID: 10 - 336

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Adenomatous polyposis coli protein / Protein APC / Deleted in polyposis 2.5


Mass: 42048.312 Da / Num. of mol.: 2 / Fragment: ARM 1-7 domain, UNP residues 407-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC, DP2.5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25054
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.34 Å3/Da / Density % sol: 47.55 % / Mosaicity: 0.431 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 1.02M Sodium phosphate monobasic monohydrate, 0.18M Potassium phosphate dibasic, vapor diffusion, hanging drop, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10096 / % possible obs: 99.1 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.058 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.920.70.559981.2211100
2.9-3.0220.90.3839911.1161100
3.02-3.1520.90.279971.0981100
3.15-3.3220.80.179990.9361100
3.32-3.5320.70.1379921.084199.9
3.53-3.820.70.09810160.987199.9
3.8-4.1820.40.0849991.013199.2
4.18-4.7920.10.06810211.043199.2
4.79-6.0319.90.06910381.065199.5
6.03-5017.80.0610451.016194.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NMW

3nmw


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 18.87 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.845 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3126 447 4.9 %RANDOM
Rwork0.2689 ---
obs0.2712 9077 53.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 60.8089 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 10 26 4807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214823
X-RAY DIFFRACTIONr_angle_refined_deg0.9081.9546506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg45612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66224.4200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38715886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0821530
X-RAY DIFFRACTIONr_chiral_restr0.0570.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023488
X-RAY DIFFRACTIONr_mcbond_it0.1071.53065
X-RAY DIFFRACTIONr_mcangle_it0.20424874
X-RAY DIFFRACTIONr_scbond_it0.32631758
X-RAY DIFFRACTIONr_scangle_it0.5324.51632
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2324 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.30.5
MEDIUM THERMAL0.142
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 32 -
Rwork0.149 617 -
all-649 -
obs--53.02 %
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)
10.75020.2452-0.28092.02882.03595.3486-0.0073-0.13110.1367-0.03580.04790.0499-0.20750.2762-0.04060.0112-0.0046-0.00630.350.09210.26259.348615.5498-30.3244
22.1526-0.71881.84160.8978-1.32895.13740.1356-0.04460.0301-0.20740.03180.03940.2717-0.3209-0.16740.1914-0.11830.05450.1168-0.0230.281417.8833-21.1603-12.8564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A405 - 734
2X-RAY DIFFRACTION2B405 - 734

+
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