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- PDB-5xa5: Crystal structure of HMP-1-HMP-2 complex -

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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


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 / Formation of the beta-catenin:TCF transactivating complex / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOB GTPase cycle ...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 / Formation of the beta-catenin:TCF transactivating complex / Transcriptional Regulation by VENTX / RUNX3 regulates WNT signaling / RHOA GTPase cycle / RHOB GTPase cycle / RHOQ GTPase cycle / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Deactivation of the beta-catenin transactivating complex / Apoptotic cleavage of cell adhesion proteins / Degradation of beta-catenin by the destruction complex / 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 / nuclear receptor binding / regulation of actin cytoskeleton organization / adherens junction / beta-catenin binding / cell-cell adhesion / actin filament binding / cell migration / regulation of protein localization / protein phosphatase 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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