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- PDB-8q4j: The crystal structure of human chloride intracellular channel pro... -

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Basic information

Entry
Database: PDB / ID: 8q4j
TitleThe crystal structure of human chloride intracellular channel protein 5 delta 57-68 F34D mutant
ComponentsChloride intracellular channel protein 5
KeywordsLIPID BINDING PROTEIN / CLIC5B / p64 / metamorphic protein
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors / stereocilium / chloride transport / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / chloride channel activity / chloride channel complex / visual perception / sensory perception of sound / female pregnancy ...Oxidoreductases; Acting on a sulfur group of donors / stereocilium / chloride transport / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / chloride channel activity / chloride channel complex / visual perception / sensory perception of sound / female pregnancy / actin cytoskeleton / cell cortex / oxidoreductase activity / apical plasma membrane / centrosome / Golgi apparatus / mitochondrion / extracellular exosome
Similarity search - Function
CLIC5, C-terminal GST domain / Intracellular chloride channel / : / CLIC-like N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chloride intracellular channel protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsManori, B. / Giladi, M. / Haitin, Y.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1653/21 Israel
CitationJournal: Nat Commun / Year: 2024
Title: Chloride intracellular channel (CLIC) proteins function as fusogens.
Authors: Manori, B. / Vaknin, A. / Vankova, P. / Nitzan, A. / Zaidel-Bar, R. / Man, P. / Giladi, M. / Haitin, Y.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chloride intracellular channel protein 5
A: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2543
Polymers51,1582
Non-polymers961
Water45025
1
B: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6752
Polymers25,5791
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chloride intracellular channel protein 5


Theoretical massNumber of molelcules
Total (without water)25,5791
Polymers25,5791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.688, 220.290, 45.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chloride intracellular channel protein 5


Mass: 25579.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZA1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 7.0, 30% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.886 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.505→45.478 Å / Num. obs: 22925 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rrim(I) all: 0.126 / Net I/σ(I): 11.8
Reflection shellResolution: 2.51→2.66 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3596 / CC1/2: 0.503 / Rrim(I) all: 1.975

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→42.42 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 1146 5 %
Rwork0.241 --
obs0.2428 22911 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 5 25 3235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053273
X-RAY DIFFRACTIONf_angle_d0.714471
X-RAY DIFFRACTIONf_dihedral_angle_d4.293469
X-RAY DIFFRACTIONf_chiral_restr0.042515
X-RAY DIFFRACTIONf_plane_restr0.01593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.620.47781380.45462619X-RAY DIFFRACTION98
2.62-2.760.39991400.36672674X-RAY DIFFRACTION100
2.76-2.930.34591430.34092693X-RAY DIFFRACTION100
2.93-3.160.38821420.35032696X-RAY DIFFRACTION100
3.16-3.470.34771460.27082720X-RAY DIFFRACTION100
3.47-3.980.28971370.22662719X-RAY DIFFRACTION100
3.98-5.010.20881470.18982756X-RAY DIFFRACTION99
5.01-42.420.22831530.20392888X-RAY DIFFRACTION100
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)
12.60250.21162.27431.82790.20114.1218-0.35230.02650.52260.44690.207-0.138-0.2438-0.1182-0.03380.60760.05340.01340.68210.02260.509419.100864.56028.6103
23.19380.4208-0.7313.57131.75654.92380.416-0.51590.47730.2645-0.22130.01320.34970.0912-0.07080.53720.01020.0360.7636-0.03820.646710.920965.865411.4924
33.466-0.78810.07282.5582-0.01561.71350.18280.4606-0.271-0.29470.04090.12190.0772-0.1789-0.15980.45780.00870.01570.585-0.0030.39819.919948.8766-2.0482
44.9522.0369-0.11385.4335-0.42750.798-0.1960.13611.47740.14720.27680.8294-0.4074-0.1582-0.10380.6950.0544-0.14040.6422-0.04221.42179.6577100.776715.6453
53.23780.76220.54013.2727-0.05062.3298-0.22110.25491.0713-0.3164-0.0381-0.4025-0.2287-0.0040.12810.5652-0.0155-0.02370.5002-0.05390.87519.632387.809614.9817
63.73770.94070.59024.52420.13282.0841-0.0105-0.58920.94740.3686-0.1468-0.4045-0.47120.14690.13830.62020.037-0.00020.6768-0.18870.767424.472286.000923.2652
72.49622.021-0.64833.0777-1.00483.23190.055-0.6290.35131.1901-0.0456-0.09230.2338-0.3214-0.02730.92930.14390.17851.1291-0.2520.83056.282180.079729.8722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 25 through 57 )
2X-RAY DIFFRACTION2chain 'B' and (resid 58 through 95 )
3X-RAY DIFFRACTION3chain 'B' and (resid 96 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 27 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 233 )
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 251 )

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