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- PDB-3e7k: Crystal Structure of an antiparallel coiled-coil tetramerization ... -

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Basic information

Entry
Database: PDB / ID: 3e7k
TitleCrystal Structure of an antiparallel coiled-coil tetramerization domain from TRPM7 channels
ComponentsTRPM7 channel
KeywordsMEMBRANE PROTEIN / Coiled-coil / antiparallel / Ion Channel / Assembly domain / TRPM channel / TRPM7
Function / homology
Function and homology information


intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / necroptotic process / monoatomic cation channel activity / ruffle / protein tetramerization ...intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / necroptotic process / monoatomic cation channel activity / ruffle / protein tetramerization / response to radiation / calcium channel activity / memory / synaptic vesicle membrane / calcium ion transport / kinase activity / actin binding / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / positive regulation of apoptotic process / protein phosphorylation / protein serine/threonine kinase activity / neuronal cell body / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
TRPM, tetramerisation domain / Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain ...TRPM, tetramerisation domain / Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / SLOG in TRPM / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ion transport domain / Ion transport protein / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsFujiwara, Y. / Minor, D.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: X-ray crystal structure of a TRPM assembly domain reveals an antiparallel four-stranded coiled-coil.
Authors: Fujiwara, Y. / Minor, D.L.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: TRPM7 channel
B: TRPM7 channel
C: TRPM7 channel
D: TRPM7 channel
E: TRPM7 channel
F: TRPM7 channel
G: TRPM7 channel
H: TRPM7 channel


Theoretical massNumber of molelcules
Total (without water)50,0338
Polymers50,0338
Non-polymers00
Water5,332296
1
A: TRPM7 channel
B: TRPM7 channel
C: TRPM7 channel
D: TRPM7 channel


Theoretical massNumber of molelcules
Total (without water)25,0164
Polymers25,0164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-97 kcal/mol
Surface area11250 Å2
MethodPISA
2
E: TRPM7 channel
F: TRPM7 channel
G: TRPM7 channel
H: TRPM7 channel


Theoretical massNumber of molelcules
Total (without water)25,0164
Polymers25,0164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-98 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.258, 35.674, 100.322
Angle α, β, γ (deg.)90.000, 124.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TRPM7 channel


Mass: 6254.092 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: 'GAGS' IS AN EXPRESSION TAG / Plasmid: pSV272 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q925B3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M MgCl2, 0.1 M Tris, 5-10% Isopropanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 19, 2006
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28234 / % possible obs: 97.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.121 / Χ2: 1.331
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.359 / Num. unique all: 2456 / Χ2: 0.928 / % possible all: 85.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.36 Å
Translation2.5 Å41.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.797 / SU B: 10.415 / SU ML: 0.148 / SU R Cruickshank DPI: 0.233 / SU Rfree: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1436 5.1 %RANDOM
Rwork0.188 ---
obs0.191 28201 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.58 Å2 / Biso mean: 27.493 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å21.46 Å2
2---0.52 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 296 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223388
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9684553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74324.323155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7915668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1931532
X-RAY DIFFRACTIONr_chiral_restr0.1190.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022420
X-RAY DIFFRACTIONr_mcbond_it1.77622127
X-RAY DIFFRACTIONr_mcangle_it2.87533446
X-RAY DIFFRACTIONr_scbond_it2.45121261
X-RAY DIFFRACTIONr_scangle_it3.79131107
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 74 -
Rwork0.234 1550 -
all-1624 -
obs--77.74 %
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)
16.6776-6.56822.09287.0577-1.9730.7147-0.1796-0.13540.12340.25410.1702-0.2015-0.0459-0.06260.0094-0.0755-0.03110.0093-0.0490.0005-0.0639-14.774911.4282-27.1146
25.7254-7.18483.89419.8701-5.32732.9387-0.1396-0.0726-0.06110.26940.14480.2658-0.0998-0.1042-0.0052-0.0644-0.01560.0234-0.0632-0.0198-0.0652-22.05558.6389-31.0951
32.5602-5.07322.216210.1638-4.49172.10550.18380.09440.0499-0.3627-0.2066-0.11540.19620.09070.0227-0.0467-0.01810.0244-0.04540.0082-0.0129-16.45016.4325-36.9444
43.7331-5.79010.90869.986-1.57140.43510.0617-0.00160.1345-0.1925-0.0298-0.17890.05370.0257-0.0319-0.0526-0.02110.0088-0.0551-0.0205-0.0518-12.817813.3429-34.881
58.90879.34090.738810.02750.57360.2344-0.12030.22480.0257-0.15850.19140.1459-0.06030.0073-0.0711-0.04840.00910.0134-0.02010.0021-0.0559-33.070129.012-15.1429
67.90588.30424.03239.52774.74642.4473-0.14030.1622-0.1892-0.20280.2529-0.3013-0.08390.0988-0.1126-0.04620.01170.0006-0.00570.0157-0.0892-25.292326.0782-12.8766
73.20525.70531.599910.75113.03180.9620.2126-0.1217-0.02860.3562-0.187-0.01840.113-0.0838-0.0256-0.04130.01070.03020.0037-0.0163-0.0416-29.425924.2159-6.0878
84.00166.24320.095710.46490.01220.07290.0975-0.020.16190.3471-0.02920.2585-0.0084-0.0594-0.0683-0.03970.0280.0242-0.0036-0.0097-0.0713-33.251431.1997-7.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 545 - 54
2X-RAY DIFFRACTION2BB5 - 545 - 54
3X-RAY DIFFRACTION3CC5 - 545 - 54
4X-RAY DIFFRACTION4DD5 - 545 - 54
5X-RAY DIFFRACTION5EE5 - 545 - 54
6X-RAY DIFFRACTION6FF5 - 545 - 54
7X-RAY DIFFRACTION7GG5 - 545 - 54
8X-RAY DIFFRACTION8HH5 - 545 - 54

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