[English] 日本語
Yorodumi
- PDB-3vvi: Crystal structure of the coiled-coil domain of the transient rece... -

+
Open data


ID or keywords:

Loading...

-
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 / homology: / : / : / TRPY1 N-terminal linker helical domain / Calcium channel YVC1-like, C-terminal / membrane / ACETATE ION / Chromosome 2, complete genome
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
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://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