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- PDB-8q4i: The crystal structure of human chloride intracellular channel pro... -

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Basic information

Entry
Database: PDB / ID: 8q4i
TitleThe crystal structure of human chloride intracellular channel protein 5 delta 57-68
ComponentsChloride intracellular channel protein 5
KeywordsLIPID BINDING PROTEIN / CLIC5B / p64 / metamorphic protein
Function / homology
Function and homology information


stereocilium base / response to stimulus / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / chloride transport / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound ...stereocilium base / response to stimulus / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / chloride transport / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound / actin cytoskeleton / cell cortex / apical plasma membrane / centrosome / Golgi apparatus / mitochondrion / extracellular exosome
Similarity search - Function
CLIC5, C-terminal GST domain / Intracellular chloride channel / Glutathione S-transferase, 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, N-terminal / 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: 2.1 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)51,4154
Polymers51,2222
Non-polymers1922
Water88349
1
B: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7072
Polymers25,6111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7072
Polymers25,6111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.128, 220.832, 45.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Chloride intracellular channel protein 5


Mass: 25611.201 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
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: 2.1→45.023 Å / Num. obs: 38486 / % possible obs: 99.8 % / Redundancy: 16.7 % / Biso Wilson estimate: 52.12 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 19.1
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3926 / CC1/2: 0.815 / Rrim(I) all: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.56 Å / SU ML: 0.3079 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 2002 5.21 %
Rwork0.2322 36407 -
obs0.2333 38409 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 10 49 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543281
X-RAY DIFFRACTIONf_angle_d0.7134477
X-RAY DIFFRACTIONf_chiral_restr0.044514
X-RAY DIFFRACTIONf_plane_restr0.0061590
X-RAY DIFFRACTIONf_dihedral_angle_d14.59841111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.40461370.38042517X-RAY DIFFRACTION97.83
2.15-2.210.3741370.34052555X-RAY DIFFRACTION99.52
2.21-2.280.35161410.33142558X-RAY DIFFRACTION99.74
2.28-2.350.36691450.29622563X-RAY DIFFRACTION99.74
2.35-2.430.30231400.27852558X-RAY DIFFRACTION99.63
2.43-2.530.24251370.23832576X-RAY DIFFRACTION99.63
2.53-2.650.26181420.22822602X-RAY DIFFRACTION99.75
2.65-2.790.28041450.23812578X-RAY DIFFRACTION99.85
2.79-2.960.31861420.26592590X-RAY DIFFRACTION99.89
2.96-3.190.34191420.27712606X-RAY DIFFRACTION99.96
3.19-3.510.29241450.24322621X-RAY DIFFRACTION100
3.51-4.020.21641450.21672629X-RAY DIFFRACTION99.96
4.02-5.060.2071500.19582666X-RAY DIFFRACTION99.96
5.06-42.560.22151540.21392788X-RAY DIFFRACTION99.83
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)
18.46540177074-1.50950900386-2.635682305187.643650001561.580583106424.473743616580.09093853759010.6317974409390.5967336160570.02687494804570.0963055308673-0.243698993759-0.1095335875370.117313201372-0.03347683308310.477767823307-0.02612817114350.01674724821820.7844678152690.04957270756340.36881047187821.760456023565.829756758412.5647375339
26.40807288308-1.29729295142-2.314659994515.894206247051.606327062745.76278797730.0127100597602-0.0663022916790.08706837970630.2118227713750.102362668490.1374151162080.245016731247-0.324735602145-0.08408239974320.3505783758740.004694814513150.02911911749150.7057705579560.01780928304610.39318301950112.355071016265.11291450279.14889351809
32.63317206983-1.31423536064-0.3506063132132.54345693322-0.3724780752361.344746846890.149436124280.425632356135-0.0249719986527-0.296724691223-0.0653720740340.07208501064070.0193500976557-0.252916127477-0.09239249997280.3916592504820.00261923769092-0.003279489106540.7021808494310.03083563488610.36141929400819.428813856949.5229267756-3.05012433016
48.480030306695.822151320190.5928587174844.31681898191-0.3629658092513.15934412064-0.246093136167-1.1298255177-1.156453874122.115636500150.233013613716-0.861462005291.27970315491-0.221664155220.0575795295120.81655030165-0.0761414612451-0.01498482700120.9566393903210.2325280770940.72326551772529.791426432138.024440631615.8823806732
55.31383910202-0.442757508079-0.6368128452863.70963529131-1.135529649824.85470661674-0.0005523807620720.1358549063731.29749544628-0.06192313496180.2734981277351.400476492510.0602578568571-0.45714624467-0.2711254158690.7572629790020.029707306852-0.1187791833990.604157724739-0.05098215216891.471779489529.62694841007100.63493921915.65186681
64.062201742711.560415592420.6771960678796.43157406467-0.7017938632363.41086030159-0.214435780413-0.3761969439450.6934513942230.09292889108170.0771147515219-0.575762459152-0.2117564355030.1679323193710.1141987928240.4146986633820.06274240443680.01587645194670.584621777075-0.1678073392310.62484415957323.519410442985.383003867520.464358571
77.435490917124.50966162534-0.7152153089098.642502339010.05178569940485.241882221840.291927635559-1.384796634541.797485697641.12409406846-0.5305613587360.918473851728-0.280156578296-0.3308142594140.246357537040.672884401970.2048738065140.05334544673560.892127805914-0.2332590055130.96786471635311.644243328188.52911763328.2464678634
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 25 through 44 )BA25 - 441 - 20
22chain 'B' and (resid 45 through 95 )BA45 - 9521 - 71
33chain 'B' and (resid 96 through 241 )BA96 - 24172 - 217
44chain 'B' and (resid 242 through 251 )BA242 - 251218 - 227
55chain 'A' and (resid 27 through 95 )AB27 - 951 - 69
66chain 'A' and (resid 96 through 223 )AB96 - 22370 - 188
77chain 'A' and (resid 224 through 250 )AB224 - 250189 - 215

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