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- PDB-5h5m: Crystal structure of HMP-1 M domain -

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Basic information

Entry
Database: PDB / ID: 5h5m
TitleCrystal structure of HMP-1 M domain
ComponentsAlpha-catenin-like protein hmp-1
KeywordsCELL ADHESION / alpha-catenin / four helix bundle
Function / homology
Function and homology information


VEGFR2 mediated vascular permeability / embryonic body morphogenesis / cell migration involved in gastrulation / cell-cell adhesion mediated by cadherin / catenin complex / apical junction complex / cortical actin cytoskeleton organization / regulation of actin cytoskeleton organization / adherens junction / beta-catenin binding ...VEGFR2 mediated vascular permeability / embryonic body morphogenesis / cell migration involved in gastrulation / cell-cell adhesion mediated by cadherin / catenin complex / apical junction complex / cortical actin cytoskeleton organization / regulation of actin cytoskeleton organization / adherens junction / beta-catenin binding / cell-cell adhesion / regulation of protein localization / actin filament binding / cell migration / cadherin binding / cytoplasm
Similarity search - Function
Alpha-catenin / Alpha-catenin/vinculin-like / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-catenin-like protein hmp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKang, H. / Bang, I. / Weis, W.I. / Choi, H.J.
Funding support Korea, Republic Of, United States, 5items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2014R1A4A10052590 Korea, Republic Of
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094663 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114462 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058038 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL127711 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and functional characterization of Caenorhabditis elegans alpha-catenin reveals constitutive binding to beta-catenin and F-actin
Authors: Kang, H. / Bang, I. / Jin, K.S. / Lee, B. / Lee, J. / Shao, X. / Heier, J.A. / Kwiatkowski, A.V. / Nelson, W.J. / Hardin, J. / Weis, W.I. / Choi, H.J.
History
DepositionNov 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Dec 14, 2022Group: Database references / Structure summary / Category: entity / struct_ref_seq_dif / Item: _entity.details / _struct_ref_seq_dif.details
Revision 1.5Dec 21, 2022Group: Structure summary / Category: pdbx_entry_details
Revision 1.6May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,7162
Polymers85,7162
Non-polymers00
Water3,567198
1
A: Alpha-catenin-like protein hmp-1


Theoretical massNumber of molelcules
Total (without water)42,8581
Polymers42,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-catenin-like protein hmp-1


Theoretical massNumber of molelcules
Total (without water)42,8581
Polymers42,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.849, 81.532, 151.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42857.875 Da / Num. of mol.: 2 / Fragment: UNP residues 270-646
Source method: isolated from a genetically manipulated source
Details: AUTHORS STATE THAT THE N-TERMINAL RESIDUES , GGIQ ARE LINKERS AFTER TAG CLEAVAGE.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hmp-1, R13H4.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P90947
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5, 0.2 M NaCl, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 36804 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.085 / Net I/av σ(I): 20.669 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.443.70.258198.9
2.44-2.493.80.234198.8
2.49-2.533.70.217198.9
2.53-2.593.70.197198.7
2.59-2.643.70.19199.1
2.64-2.73.70.165199.5
2.7-2.773.70.161199.3
2.77-2.853.70.146199.2
2.85-2.933.80.131199.5
2.93-3.023.80.123199.7
3.02-3.133.80.109199.7
3.13-3.263.90.101199.9
3.26-3.413.90.091199.9
3.41-3.583.90.0841100
3.58-3.813.80.078199.9
3.81-4.13.80.07199.8
4.1-4.523.80.066199.7
4.52-5.173.80.06199.7
5.17-6.513.70.06199.9
6.51-203.40.052195.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å27.16 Å
Translation3 Å27.16 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→27.162 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2477 1793 5.01 %
Rwork0.2029 --
obs0.2052 35763 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.75 Å2 / Biso mean: 44.1854 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 2.4→27.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5587 0 0 198 5785
Biso mean---38.38 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045652
X-RAY DIFFRACTIONf_angle_d0.777629
X-RAY DIFFRACTIONf_chiral_restr0.027888
X-RAY DIFFRACTIONf_plane_restr0.0041008
X-RAY DIFFRACTIONf_dihedral_angle_d13.5522143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46480.28691520.21982517266999
2.4648-2.53730.27711430.22092559270299
2.5373-2.61920.29351200.21092589270999
2.6192-2.71270.3121330.22612596272999
2.7127-2.82120.29161500.23452548269899
2.8212-2.94940.31161210.23425912712100
2.9494-3.10470.29571120.229326202732100
3.1047-3.2990.28561450.227926212766100
3.299-3.55320.2221270.213926312758100
3.5532-3.90980.22411470.193926362783100
3.9098-4.47340.1921410.172526332774100
4.4734-5.62770.25551510.182926762827100
5.6277-27.16340.20391510.17842753290498
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)
12.501-0.8845-3.6811.54892.11448.36270.0411-0.3228-0.00210.2188-0.15610.1070.0365-0.27030.12710.2368-0.0607-0.02220.3651-0.03040.242470.903387.175326.3177
23.5853-2.6509-1.78894.25991.47982.89260.21630.26490.0572-0.5478-0.2157-0.22750.13070.10880.00640.2890.02570.01420.18290.05080.194685.430667.9792-3.6307
35.87043.2058-0.11282.53630.06580.945-0.28810.29440.0582-0.27720.1993-0.1207-0.09730.07820.06710.26120.0077-0.00440.13780.00860.230284.196993.6876-6.7067
43.07160.0373-1.16493.99772.97028.66190.0475-0.41280.34980.3862-0.27240.3217-0.0261-0.50480.23130.2562-0.0286-0.06780.2645-0.01560.373451.901678.07656.1747
52.1493-0.5413-1.22154.18112.94294.7494-0.06060.1551-0.0647-0.24260.0428-0.08230.3283-0.21170.03690.3352-0.0656-0.06060.2910.09640.263648.144257.7797-25.1246
63.9885-0.5249-0.2733.65021.00194.0889-0.12261.14480.4302-0.37540.0721-0.3914-0.09540.21570.04810.3683-0.1347-0.08040.57290.1210.361764.617979.4274-26.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 270 through 387 )A270 - 387
2X-RAY DIFFRACTION2chain 'A' and (resid 388 through 499 )A388 - 499
3X-RAY DIFFRACTION3chain 'A' and (resid 500 through 641 )A500 - 641
4X-RAY DIFFRACTION4chain 'B' and (resid 270 through 387 )B270 - 387
5X-RAY DIFFRACTION5chain 'B' and (resid 388 through 499 )B388 - 499
6X-RAY DIFFRACTION6chain 'B' and (resid 500 through 640 )B500 - 640

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