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- PDB-5h35: Crystal structures of the TRIC trimeric intracellular cation chan... -

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Basic information

Entry
Database: PDB / ID: 5h35
TitleCrystal structures of the TRIC trimeric intracellular cation channel orthologue from Sulfolobus solfataricus
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • Membrane protein TRICBiological membrane
KeywordsIMMUNE SYSTEM/MEMBRANE PROTEIN / ion channels / IMMUNE SYSTEM-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


membrane => GO:0016020 / plasma membrane
Similarity search - Function
Glycine transporter / Glycine transporter / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Membrane protein / Glycine transporter domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.642 Å
AuthorsKasuya, G. / Hiraizumi, M. / Hattori, M. / Nureki, O.
CitationJournal: Cell Res. / Year: 2016
Title: Crystal structures of the TRIC trimeric intracellular cation channel orthologues
Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / ...Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / Takemoto, M. / Kato, H.E. / Yamashita, K. / Wada, M. / Ito, K. / Ishitani, R. / Hattori, M. / Nureki, O.
History
DepositionOct 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy Chain
B: Fab Light Chain
C: Membrane protein TRIC
D: Membrane protein TRIC
E: Membrane protein TRIC
F: Fab Heavy Chain
G: Fab Light Chain
H: Fab Heavy Chain
I: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,32515
Polymers218,0819
Non-polymers2,2446
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23710 Å2
ΔGint-167 kcal/mol
Surface area75440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.734, 171.391, 103.265
Angle α, β, γ (deg.)90.00, 117.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules CDE

#3: Protein Membrane protein TRIC / Biological membrane / Uncharacterized protein


Mass: 23070.096 Da / Num. of mol.: 3 / Fragment: UNP residues 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MGX1, UniProt: Q981D4*PLUS

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Antibody , 2 types, 6 molecules AFHBGI

#1: Antibody Fab Heavy Chain / Fragment antigen-binding


Mass: 25357.771 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 24265.936 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 149 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG4000, MgCl2, NaCl, Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 90876 / % possible obs: 98.2 % / Redundancy: 7.02 % / Net I/σ(I): 14.59

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 2.642→49.404 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.252 4570 5.03 %
Rwork0.2106 --
obs0.2127 90856 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.642→49.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14438 0 55 143 14636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114853
X-RAY DIFFRACTIONf_angle_d1.3520192
X-RAY DIFFRACTIONf_dihedral_angle_d16.4755202
X-RAY DIFFRACTIONf_chiral_restr0.0592326
X-RAY DIFFRACTIONf_plane_restr0.0072506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6419-2.67190.35851490.34252688X-RAY DIFFRACTION93
2.6719-2.70340.38561510.32292906X-RAY DIFFRACTION99
2.7034-2.73630.35541520.3042857X-RAY DIFFRACTION99
2.7363-2.7710.35731420.29822890X-RAY DIFFRACTION99
2.771-2.80740.32461650.28232883X-RAY DIFFRACTION99
2.8074-2.84590.32771370.28822866X-RAY DIFFRACTION98
2.8459-2.88650.3591670.28562762X-RAY DIFFRACTION96
2.8865-2.92960.33541230.27582931X-RAY DIFFRACTION99
2.9296-2.97540.33361660.26442856X-RAY DIFFRACTION99
2.9754-3.02420.34781540.27422906X-RAY DIFFRACTION99
3.0242-3.07630.2921700.26972869X-RAY DIFFRACTION99
3.0763-3.13220.34441300.26092928X-RAY DIFFRACTION99
3.1322-3.19250.35711560.25812855X-RAY DIFFRACTION99
3.1925-3.25760.25431470.23832908X-RAY DIFFRACTION99
3.2576-3.32840.271520.23112912X-RAY DIFFRACTION99
3.3284-3.40580.28711540.21712828X-RAY DIFFRACTION99
3.4058-3.4910.27041450.21832853X-RAY DIFFRACTION98
3.491-3.58530.27521520.21282812X-RAY DIFFRACTION96
3.5853-3.69080.22141520.20442939X-RAY DIFFRACTION100
3.6908-3.80990.22421600.1932901X-RAY DIFFRACTION99
3.8099-3.9460.24561520.19982896X-RAY DIFFRACTION99
3.946-4.10390.23831560.1842902X-RAY DIFFRACTION99
4.1039-4.29060.21091640.17632859X-RAY DIFFRACTION99
4.2906-4.51670.21831570.17712863X-RAY DIFFRACTION99
4.5167-4.79940.23651610.18122843X-RAY DIFFRACTION97
4.7994-5.16960.22681430.17992944X-RAY DIFFRACTION100
5.1696-5.68920.2661550.18852933X-RAY DIFFRACTION100
5.6892-6.51090.2191630.18782866X-RAY DIFFRACTION99
6.5109-8.19690.22631450.18862892X-RAY DIFFRACTION98
8.1969-49.4130.19391500.20942938X-RAY DIFFRACTION98

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