[English] 日本語
Yorodumi
- PDB-5xa5: Crystal structure of HMP-1-HMP-2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xa5
TitleCrystal structure of HMP-1-HMP-2 complex
Components
  • Alpha-catenin-like protein hmp-1
  • Beta-catenin-like protein hmp-2
KeywordsCELL ADHESION / five-helix bundle
Function / homology
Function and homology information


Degradation of beta-catenin by the destruction complex / Beta-catenin phosphorylation cascade / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Formation of the cornified envelope / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOB GTPase cycle ...Degradation of beta-catenin by the destruction complex / Beta-catenin phosphorylation cascade / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Formation of the cornified envelope / RHOH GTPase cycle / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOB GTPase cycle / RHOQ GTPase cycle / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / Apoptotic cleavage of cell adhesion proteins / VEGFR2 mediated vascular permeability / Ca2+ pathway / Neutrophil degranulation / embryonic body morphogenesis / cell migration involved in gastrulation / left/right axis specification / negative regulation of cell division / cell-cell adhesion mediated by cadherin / alpha-catenin binding / catenin complex / embryo development ending in birth or egg hatching / apical junction complex / cortical actin cytoskeleton organization / molecular function inhibitor activity / establishment of mitotic spindle orientation / canonical Wnt signaling pathway / regulation of actin cytoskeleton organization / adherens junction / beta-catenin binding / cell-cell adhesion / regulation of protein localization / actin filament binding / cell migration / protein phosphatase binding / DNA-binding transcription factor binding / transcription coactivator activity / cadherin binding / protein domain specific binding / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Alpha-catenin / Beta-catenin / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Beta-catenin-like protein hmp-2 / Alpha-catenin-like protein hmp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsShao, X. / Kang, H. / Weis, W.I. / Hardin, J. / Choi, H.J.
CitationJournal: J.Biol.Chem. / Year: 2017
Title: Cell-cell adhesion in metazoans relies on evolutionarily conserved features of the alpha-catenin· beta-catenin-binding interface.
Authors: Shao, X. / Kang, H. / Loveless, T. / Lee, G.R. / Seok, C. / Weis, W.I. / Choi, H.J. / Hardin, J.
History
DepositionMar 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-catenin-like protein hmp-1
B: Beta-catenin-like protein hmp-2


Theoretical massNumber of molelcules
Total (without water)35,9842
Polymers35,9842
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-30 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.095, 57.095, 155.436
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-497-

HOH

-
Components

#1: Protein Alpha-catenin-like protein hmp-1 / Protein humpback-1


Mass: 30899.760 Da / Num. of mol.: 1 / Fragment: UNP residues 2-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hmp-1, R13H4.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P90947
#2: Protein/peptide Beta-catenin-like protein hmp-2 / Protein humpback-2


Mass: 5084.645 Da / Num. of mol.: 1 / Fragment: UNP residues 36-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hmp-2, K05C4.6 / Production host: Escherichia coli (E. coli) / References: UniProt: O44326
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate pH 5.6, 0.2M lithium sulfate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.006 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.577→38.859 Å / Num. obs: 40755 / % possible obs: 98.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 28.48 Å2 / Rpim(I) all: 0.014 / Rrim(I) all: 0.033 / Rsym value: 0.03 / Net I/av σ(I): 10.6 / Net I/σ(I): 23.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.58-1.664.50.5551.40.2860.6270.55590.3
1.66-1.765.50.3642.10.170.4030.364100
1.76-1.895.30.194.10.0910.2110.1999.9
1.89-2.045.50.1077.20.050.1180.10799.9
2.04-2.235.30.05613.20.0270.0620.05699.7
2.23-2.495.30.03918.20.0190.0430.03999.5
2.49-2.885.30.0322.30.0140.0330.0399.7
2.88-3.535.30.02523.40.0120.0280.02599.9
3.53-4.9950.02226.50.010.0250.02299.6
4.99-38.8594.80.02120.40.010.0230.02199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
SCALA3.3.16data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.547 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.2228 1977 5.01 %
Rwork0.1896 --
obs0.1912 39456 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.08 Å2 / Biso mean: 41.2515 Å2 / Biso min: 18.18 Å2
Refinement stepCycle: final / Resolution: 1.6→28.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 220 2365
Biso mean---47.48 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072259
X-RAY DIFFRACTIONf_angle_d0.9673091
X-RAY DIFFRACTIONf_chiral_restr0.034385
X-RAY DIFFRACTIONf_plane_restr0.005403
X-RAY DIFFRACTIONf_dihedral_angle_d13.676884
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.30171360.26712590272698
1.64-1.68440.29091250.234126602785100
1.6844-1.73390.26471550.226526532808100
1.7339-1.78990.30381400.2226572797100
1.7899-1.85380.24141350.209326332768100
1.8538-1.9280.24191390.24762573271298
1.928-2.01580.24721310.212227092840100
2.0158-2.1220.22181400.208426792819100
2.122-2.25490.20751270.20832627275498
2.2549-2.42890.26031350.190826692804100
2.4289-2.67320.23681460.201227072853100
2.6732-3.05960.23131650.19792681284699
3.0596-3.85330.2111500.179827552905100
3.8533-28.5520.1961530.16242886303999
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)
11.1742-0.2326-1.11191.26450.39041.7991-0.1473-0.2557-0.10670.24870.1153-0.05710.39650.27780.00520.40180.12030.03920.31980.02740.267916.074-6.548124.3856
20.9495-0.6651-0.98941.57152.0551.9532-0.2365-0.43090.09270.51780.4296-0.21050.39970.5412-0.12120.47140.2103-0.05250.407-0.02270.221723.9272-11.640723.8075
31.044-0.4034-0.35742.34420.75711.74810.04860.1571-0.0329-0.14950.0999-0.19-0.146-0.0038-0.12650.160.02970.03460.2654-0.02560.240328.0458-26.0689-7.3706
42.4418-1.6996-1.92915.17413.08523.66620.0636-0.0863-0.1293-0.0546-0.38070.51830.0195-0.25460.26660.39180.09520.03120.2815-0.01460.209611.9285-4.630625.8589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 78 )A13 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 161 )A79 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 260 )A162 - 260
4X-RAY DIFFRACTION4chain 'B' and (resid 46 through 72 )B46 - 72

+
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://pdbjlvh1.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