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- PDB-6y2h: The crystal structure of human chloride intracellular channel pro... -

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Basic information

Entry
Database: PDB / ID: 6y2h
TitleThe crystal structure of human chloride intracellular channel protein 5
ComponentsChloride intracellular channel protein 5
KeywordsTRANSPORT PROTEIN / Chloride intracellular channel / CLIC / metamorphic protein
Function / homology
Function and homology information


stereocilium base / Oxidoreductases; Acting on a sulfur group of donors / Sensory processing of sound by outer hair cells of the cochlea / chloride transport / Sensory processing of sound by inner hair cells of the cochlea / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound ...stereocilium base / Oxidoreductases; Acting on a sulfur group of donors / Sensory processing of sound by outer hair cells of the cochlea / chloride transport / Sensory processing of sound by inner hair cells of the cochlea / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound / actin cytoskeleton / cell cortex / oxidoreductase activity / mitochondrial inner membrane / apical plasma membrane / centrosome / Golgi apparatus / extracellular exosome
Similarity search - Function
CLIC5, C-terminal GST domain / Intracellular chloride channel / : / CLIC-like N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like ...CLIC5, C-terminal GST domain / Intracellular chloride channel / : / CLIC-like N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Chloride intracellular channel protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsFerofontov, A. / Giladi, M. / Haitin, Y.
Funding support Israel, 4items
OrganizationGrant numberCountry
Israel Science Foundation1721/16 Israel
Israel Science Foundation1775/12 Israel
German-Israeli Foundation for Research and DevelopmentI-2425-418.13/2016 Israel
Other privateICRF 01214 Israel
CitationJournal: Faseb J. / Year: 2020
Title: Conserved cysteine dioxidation enhances membrane interaction of human Cl - intracellular channel 5.
Authors: Ferofontov, A. / Vankova, P. / Man, P. / Giladi, M. / Haitin, Y.
History
DepositionFeb 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,58217
Polymers107,8274
Non-polymers75513
Water6,864381
1
A: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1314
Polymers26,9571
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3057
Polymers26,9571
Non-polymers3486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1314
Polymers26,9571
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chloride intracellular channel protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0152
Polymers26,9571
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.990, 93.960, 109.580
Angle α, β, γ (deg.)90.000, 124.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 14 through 20 or (resid 21...
21(chain B and ((resid 14 and (name N or name...
31(chain C and ((resid 14 and (name N or name...
41(chain D and (resid 14 through 20 or (resid 21...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVAL(chain A and (resid 14 through 20 or (resid 21...AA14 - 203 - 9
12LYSLYSLYSLYS(chain A and (resid 14 through 20 or (resid 21...AA2110
13METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
14METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
15METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
16METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
17METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
18METMETSERSER(chain A and (resid 14 through 20 or (resid 21...AA14 - 2493 - 238
21METMETMETMET(chain B and ((resid 14 and (name N or name...BB143
22GLYGLYARGARG(chain B and ((resid 14 and (name N or name...BB12 - 2471 - 236
23GLYGLYARGARG(chain B and ((resid 14 and (name N or name...BB12 - 2471 - 236
24GLYGLYARGARG(chain B and ((resid 14 and (name N or name...BB12 - 2471 - 236
25GLYGLYARGARG(chain B and ((resid 14 and (name N or name...BB12 - 2471 - 236
31METMETMETMET(chain C and ((resid 14 and (name N or name...CC143
32GLYGLYLEULEU(chain C and ((resid 14 and (name N or name...CC12 - 2481 - 237
33GLYGLYLEULEU(chain C and ((resid 14 and (name N or name...CC12 - 2481 - 237
34GLYGLYLEULEU(chain C and ((resid 14 and (name N or name...CC12 - 2481 - 237
35GLYGLYLEULEU(chain C and ((resid 14 and (name N or name...CC12 - 2481 - 237
41METMETVALVAL(chain D and (resid 14 through 20 or (resid 21...DD14 - 203 - 9
42LYSLYSLYSLYS(chain D and (resid 14 through 20 or (resid 21...DD2110
43ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
44ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
45ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
46ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
47ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
48ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
49ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
410ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
411ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238
412ALAALASERSER(chain D and (resid 14 through 20 or (resid 21...DD13 - 2492 - 238

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Components

#1: Protein
Chloride intracellular channel protein 5


Mass: 26956.799 Da / Num. of mol.: 4
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.1M NaSCN, 17%PEG 3350, 7% MEG

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: With 20% MEG as cryoprotectant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→48.005 Å / Num. obs: 65103 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.4
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 1.52 / Num. unique obs: 12363

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHE

2ahe


Resolution: 2.154→48.005 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.77
RfactorNum. reflection% reflection
Rfree0.2443 2494 5.06 %
Rwork0.201 --
obs0.2033 49260 82.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.71 Å2 / Biso mean: 48.3791 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: final / Resolution: 2.154→48.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6541 0 39 381 6961
Biso mean--63.7 48.8 -
Num. residues----869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2444X-RAY DIFFRACTION8.652TORSIONAL
12B2444X-RAY DIFFRACTION8.652TORSIONAL
13C2444X-RAY DIFFRACTION8.652TORSIONAL
14D2444X-RAY DIFFRACTION8.652TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1543-2.19580.479890.23282247
2.1958-2.24060.2517360.233965821
2.2406-2.28930.2555610.2577133042
2.2893-2.34250.325990.2738208867
2.3425-2.40110.29141530.2678261385
2.4011-2.4660.2941430.272301095
2.466-2.53860.32211690.2497309899
2.5386-2.62050.29681670.2291313099
2.6205-2.71420.27441420.2252308699
2.7142-2.82290.2621720.2212309099
2.8229-2.95130.26011720.2256310299
2.9513-3.10690.26851650.2168308198
3.1069-3.30150.26381770.2161299096
3.3015-3.55630.23831750.192304598
3.5563-3.91410.22121500.1723308797
3.9141-4.48010.20091670.1583304497
4.4801-5.6430.22191780.1708298795
5.643-48.0050.22491590.1978310396
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)
13.8232-2.8228-0.35227.9065-6.59998.739-0.8564-0.02070.75960.7757-0.1842-0.3068-1.3388-0.76661.13221.10170.14030.14990.504-0.09521.146-12.346119.435947.4021
23.3779-1.73370.44242.8123-2.02385.1010.1565-0.1507-0.3839-0.0403-0.06610.77660.0289-0.4224-0.07680.2669-0.01310.07570.28-0.08830.395724.52814.47897.3133
32.209-0.35081.46350.0841-0.63836.84730.03440.7138-0.8962-0.39030.47940.74260.9372-0.6298-0.32730.4445-0.03810.03130.4945-0.16710.7719.391512.93123.5612
42.9951-0.7569-0.42293.4423-1.1263.47520.1350.0717-0.1418-0.0854-0.3107-0.08570.01190.27240.12930.2494-0.02750.03950.2241-0.08960.239438.485213.44382.8346
53.2584-0.8533-0.22293.0349-0.41343.69510.096-0.30640.04540.5071-0.2074-0.1549-0.24440.4550.10820.2443-0.0858-0.02520.3332-0.02410.27241.115214.439213.6116
63.1431-0.4906-1.09575.4214-0.01354.12750.0186-0.0187-0.2127-0.1152-0.1671-0.52930.14890.28710.10820.1963-0.0283-0.00430.19750.02380.255749.6104-7.9741-12.7416
72.34840.3555-0.40194.31310.46014.72280.1863-0.01350.2371-0.18860.05030.0253-0.96030.0955-0.13150.3122-0.02520.02220.2253-0.02910.251946.610112.407-15.4311
81.844-0.3382-0.35128.2858-0.6772.92090.23440.2010.1569-0.2744-0.11760.4914-0.5503-0.1406-0.13430.32050.00010.09570.2497-0.03210.34667.416119.022124.9727
92.8890.09330.2433.76520.54553.61250.0392-0.191-0.28110.0541-0.1146-0.00560.30210.0450.04830.2631-0.03830.06520.17430.02910.299211.2205-1.845326.6152
105.7637-1.66590.95728.3407-0.57696.6187-0.3395-1.0170.381.31580.12010.0894-0.24290.06040.40630.5432-0.0550.04960.39870.05370.3371-1.0437-0.492760.037
113.6609-0.69590.34886.09830.32554.2157-0.2958-0.2166-0.29860.1094-0.195-0.22670.5493-0.02130.21320.4713-0.06630.19530.23170.05680.3068-1.1689-8.318953.8535
127.7238-2.2997-1.66185.2473-1.86768.5791-0.0516-0.74320.5847-0.4298-0.1571-1.0278-0.09661.7120.18570.5031-0.19190.00280.73540.11710.44959.6937-3.117955.5451
133.8829-0.65320.84289.24.30659.5618-0.5347-0.022-0.4151-10.106-0.14010.02230.9450.36120.5376-0.06370.11310.35920.07480.38268.223-9.248245.9968
142.685-0.7374-0.23810.19760.02813.8661-0.12490.3231-0.4096-0.2279-0.10870.1010.70770.17670.08020.5518-0.08070.15140.2726-0.07320.48930.1135-13.566439.8668
155.1148-1.8332-0.85696.88861.25024.9040.51231.03030.6001-1.0205-0.29920.3372-0.8577-1.3045-0.07160.57740.10220.0630.69040.10660.4514-13.07888.013835.3044
161.899-1.11060.75753.2016-1.66360.88960.3340.6113-0.9608-0.3192-0.31960.78440.8601-0.68680.15040.6037-0.25450.15280.6229-0.36280.7195-11.2365-15.45335.2644
173.5905-1.9592-0.63955.4724-1.33983.6104-0.21620.4972-0.10570.4244-0.03510.79760.1343-1.06840.20050.3456-0.08710.120.4943-0.10130.513-14.4777-0.608945.9558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 242 through 249 )D242 - 249
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 45 )A14 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 73 )A46 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 153 )A74 - 153
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 249 )A154 - 249
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 95 )B12 - 95
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 247 )B96 - 247
8X-RAY DIFFRACTION8chain 'C' and (resid 12 through 95 )C12 - 95
9X-RAY DIFFRACTION9chain 'C' and (resid 96 through 248 )C96 - 248
10X-RAY DIFFRACTION10chain 'D' and (resid 13 through 32 )D13 - 32
11X-RAY DIFFRACTION11chain 'D' and (resid 33 through 53 )D33 - 53
12X-RAY DIFFRACTION12chain 'D' and (resid 54 through 84 )D54 - 84
13X-RAY DIFFRACTION13chain 'D' and (resid 85 through 95 )D85 - 95
14X-RAY DIFFRACTION14chain 'D' and (resid 96 through 117 )D96 - 117
15X-RAY DIFFRACTION15chain 'D' and (resid 118 through 153 )D118 - 153
16X-RAY DIFFRACTION16chain 'D' and (resid 154 through 182 )D154 - 182
17X-RAY DIFFRACTION17chain 'D' and (resid 183 through 241 )D183 - 241

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