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- PDB-3vvi: Crystal structure of the coiled-coil domain of the transient rece... -

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Basic information

Entry
Database: PDB / ID: 3vvi
TitleCrystal structure of the coiled-coil domain of the transient receptor potential channel from Gibberella zeae (TRPGz)
ComponentsNon selective cation channel homologous to TRP channel
KeywordsTRANSPORT PROTEIN / coiled-coil / regulation of the channel function / ion channel / osomosensor
Function / homologyPolycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Transient receptor potential cation channel subfamily V / monoatomic ion channel activity / membrane => GO:0016020 / ACETATE ION / PKD_channel domain-containing protein
Function and homology information
Biological speciesGibberella zeae PH-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsIhara, M. / Yamashita, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel
Authors: Ihara, M. / Hamamoto, S. / Miyanoiri, Y. / Takeda, M. / Kainosho, M. / Yabe, I. / Uozumi, N. / Yamashita, A.
History
DepositionJul 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non selective cation channel homologous to TRP channel
B: Non selective cation channel homologous to TRP channel
C: Non selective cation channel homologous to TRP channel
D: Non selective cation channel homologous to TRP channel
E: Non selective cation channel homologous to TRP channel
F: Non selective cation channel homologous to TRP channel
G: Non selective cation channel homologous to TRP channel
H: Non selective cation channel homologous to TRP channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,80111
Polymers19,6248
Non-polymers1773
Water4,486249
1
A: Non selective cation channel homologous to TRP channel
B: Non selective cation channel homologous to TRP channel
C: Non selective cation channel homologous to TRP channel
D: Non selective cation channel homologous to TRP channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8715
Polymers9,8124
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-41 kcal/mol
Surface area6400 Å2
MethodPISA
2
E: Non selective cation channel homologous to TRP channel
F: Non selective cation channel homologous to TRP channel
G: Non selective cation channel homologous to TRP channel
H: Non selective cation channel homologous to TRP channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9306
Polymers9,8124
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-42 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.290, 35.290, 120.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide
Non selective cation channel homologous to TRP channel / transient receptor potential channel


Mass: 2452.955 Da / Num. of mol.: 8 / Fragment: coiled-coil domain, UNP residues 600-620 / Source method: obtained synthetically
Details: This sequence is for the coiled-coil domain of the TRP channel from Gibberella zeae
Source: (synth.) Gibberella zeae PH-1 (fungus) / References: UniProt: I1RJZ4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18-25% PEG3350, 0.2M sodium acetate, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97909, 0.97944, 0.99159
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 27, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si (111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979091
20.979441
30.991591
ReflectionResolution: 1.25→35 Å / Num. obs: 40607 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 45.3
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2018 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.25→24.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.678 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.055 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19991 2015 5 %RANDOM
Rwork0.14637 ---
obs0.14903 38548 99.7 %-
Solvent computationIon probe radii: 0.4 Å / Shrinkage radii: 0.4 Å / VDW probe radii: 0.6 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 12 249 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.992.0682097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5465223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46623.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3621520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr5.14931557
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded16.96451531
LS refinement shellResolution: 1.248→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 161 -
Rwork0.1 2733 -
obs-2733 97.64 %
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)
10.0390.01320.06030.0153-0.01960.2671-0.0036-0.00160.00040.0019-0.00270.0028-0.0069-0.00130.00630.02490.0010.00050.0248-0.00050.0136-23.480421.8577-10.5278
20.0210.0110.00830.09830.03490.33310.0024-0.0016-0.00090.0041-0.00050.00310.0035-0.0069-0.00190.0211-0.000300.0220.00050.0149-22.137111.8637-7.831
30.0832-0.0157-0.04670.0385-0.01520.08870.00160.00020.00030.0022-0.0023-0.00280.00190.00640.00070.02230.000100.0220.00020.0146-13.13412.0856-5.6459
40.056-0.02050.09280.0253-0.08030.4307-0.00070.0003-0.00190.0025-0.0004-0.0009-0.00880.00360.00110.02160.0006-0.00060.0216-0.00010.0126-11.734522.2073-3.1494
50.0494-0.0564-0.07690.14870.16960.33810.00290.00370.0042-0.0038-0.004-0.0036-0.0146-0.01070.00110.0212-0.0004-0.00010.02160.00030.0133-39.48995.888511.3208
60.0039-0.0122-0.00430.0707-0.04640.11910.00010.00080.0004-0.0027-0.0002-0.0033-0.00170.00250.00010.022-0.00050.00060.022800.0149-29.54634.5228.5427
70.0538-0.0018-0.00650.00030.00110.28380.00010.00120.00220.00020.0025-0.00140.00670.0133-0.00260.024900.00080.0233-0.00020.0136-29.8032-4.50916.3255
80.0528-0.0338-0.17710.02420.12830.7304-0.0094-0.0007-0.0090.0022-0.0030.00320.0160.00720.01240.02150.001-0.00050.02210.00030.0139-39.9474-5.77483.8429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 21
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 21
5X-RAY DIFFRACTION5E1 - 21
6X-RAY DIFFRACTION6F1 - 21
7X-RAY DIFFRACTION7G1 - 21
8X-RAY DIFFRACTION8H1 - 21

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