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- PDB-6pyo: Calcium Activated Chloride Channel Regulator 1 (CLCA1) VWA Domain -

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Basic information

Entry
Database: PDB / ID: 6pyo
TitleCalcium Activated Chloride Channel Regulator 1 (CLCA1) VWA Domain
ComponentscDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA
KeywordsPROTEIN TRANSPORT / Chloride channel regulator / ion channel regulator / VWA domain
Function / homology
Function and homology information


zymogen granule membrane / intracellularly calcium-gated chloride channel activity / Hydrolases; Acting on peptide bonds (peptidases) / chloride channel activity / microvillus / metalloendopeptidase activity / Stimuli-sensing channels / metallopeptidase activity / calcium ion transport / monoatomic ion transmembrane transport ...zymogen granule membrane / intracellularly calcium-gated chloride channel activity / Hydrolases; Acting on peptide bonds (peptidases) / chloride channel activity / microvillus / metalloendopeptidase activity / Stimuli-sensing channels / metallopeptidase activity / calcium ion transport / monoatomic ion transmembrane transport / cellular response to hypoxia / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Calcium-activated chloride channel protein, chordata / Calcium-activated chloride channel, N-terminal / Calcium-activated chloride channel N terminal / : / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Calcium-activated chloride channel regulator 1 / Calcium-activated chloride channel regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrett, T.J. / Berry, K.B.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL119813 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR002345 United States
Other privateCFF BRETT-G018 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F30-HL140783 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32-HL007317 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM007200 United States
CitationJournal: Cell Rep / Year: 2020
Title: Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement.
Authors: Berry, K.N. / Brett, T.J.
History
DepositionJul 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA
B: cDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6954
Polymers39,6142
Non-polymers802
Water2,666148
1
A: cDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8873
Polymers19,8071
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA


Theoretical massNumber of molelcules
Total (without water)19,8071
Polymers19,8071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.860, 71.780, 74.840
Angle α, β, γ (deg.)90.000, 109.761, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-870-

HOH

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Components

#1: Protein cDNA FLJ56608, highly similar to Homo sapiens chloride channel, calcium activated, family member 1 (CLCA1), mRNA


Mass: 19807.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell (production host): Epithelial / Cell line (production host): Expi293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Embryonic Kidney / References: UniProt: B4DUZ6, UniProt: A8K7I4*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.91 Å3/Da / Density % sol: 68.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M HEPES pH 7.5, 0.1 M CaCl2, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 9, 2017
RadiationMonochromator: Sagittally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→58.05 Å / Num. obs: 34813 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.814 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2257 / CC1/2: 0.507 / Rpim(I) all: 0.996 / Rrim(I) all: 2.085 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCK

4rck


Resolution: 2→58.05 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 25.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1735 5.05 %random selection
Rwork0.1974 ---
obs0.1987 34366 97.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2→58.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 2 148 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122366
X-RAY DIFFRACTIONf_angle_d1.18063196
X-RAY DIFFRACTIONf_chiral_restr0.0656383
X-RAY DIFFRACTIONf_plane_restr0.0071415
X-RAY DIFFRACTIONf_dihedral_angle_d15.57431432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.3931110.35562026X-RAY DIFFRACTION73.13
2.06-2.130.32491440.30922634X-RAY DIFFRACTION94.68
2.13-2.20.29081680.2572761X-RAY DIFFRACTION99.83
2.2-2.290.27281340.25662788X-RAY DIFFRACTION99.83
2.29-2.390.22141560.20362783X-RAY DIFFRACTION99.9
2.39-2.520.21641330.1942817X-RAY DIFFRACTION100
2.52-2.680.23021550.19692781X-RAY DIFFRACTION99.9
2.68-2.880.22751290.20172840X-RAY DIFFRACTION99.83
2.88-3.170.27431590.21682773X-RAY DIFFRACTION99.8
3.17-3.630.23611570.1872777X-RAY DIFFRACTION99.53
3.63-4.580.19441410.1562794X-RAY DIFFRACTION98.49
4.58-58.070.18191480.1862857X-RAY DIFFRACTION99.34

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