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- PDB-5t5n: Calcium-activated chloride channel bestrophin-1 (BEST1), triple m... -

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Basic information

Entry
Database: PDB / ID: 5t5n
TitleCalcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A, F80A, F84A; in complex with an Fab antibody fragment, chloride, and calcium
Components
  • (Fab antibody fragment, ...) x 2
  • bestrophin-1 (BEST1)
KeywordsMEMBRANE PROTEIN / ion channel / anion / chloride / calcium-activated / eukaryotic membrane protein / CaCC
Function / homology
Function and homology information


Stimuli-sensing channels / chloride channel activity / membrane / metal ion binding
Similarity search - Function
Bestrophin-1 / Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLong, S.B. / Vaisey, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110396 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel.
Authors: Vaisey, G. / Miller, A.N. / Long, S.B.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bestrophin-1 (BEST1)
B: bestrophin-1 (BEST1)
C: bestrophin-1 (BEST1)
D: bestrophin-1 (BEST1)
E: bestrophin-1 (BEST1)
F: Fab antibody fragment, light chain (10D10)
G: Fab antibody fragment, heavy chain (10D10)
H: Fab antibody fragment, light chain (10D10)
I: Fab antibody fragment, heavy chain (10D10)
J: Fab antibody fragment, light chain (10D10)
K: Fab antibody fragment, heavy chain (10D10)
L: Fab antibody fragment, light chain (10D10)
M: Fab antibody fragment, heavy chain (10D10)
N: Fab antibody fragment, light chain (10D10)
O: Fab antibody fragment, heavy chain (10D10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,38045
Polymers471,99215
Non-polymers1,38830
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area86390 Å2
ΔGint-726 kcal/mol
Surface area140770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.243, 243.878, 172.052
Angle α, β, γ (deg.)90.00, 93.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
bestrophin-1 (BEST1)


Mass: 47420.070 Da / Num. of mol.: 5 / Mutation: I76A, F80A, F84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Pichia (fungus) / References: UniProt: E1C3A0

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Antibody , 2 types, 10 molecules FHJLNGIKMO

#2: Antibody
Fab antibody fragment, light chain (10D10)


Mass: 23339.707 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma
#3: Antibody
Fab antibody fragment, heavy chain (10D10)


Mass: 23638.525 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma

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Non-polymers , 5 types, 40 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 6% Peg 4000 50 mM sodium acetate pH 4.0 20% glycerol 75 mM NaCl 75 mM KCl 10 mM Tris-HCl pH 7.5 0.5 mM Cymal-6-NG (Anatrace)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→38 Å / Num. obs: 145877 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 82 Å2 / Net I/σ(I): 9.7
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.604 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
CNS1.3refinement
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4RDQ

4rdq


Resolution: 3.1→37.952 Å / Cross valid method: THROUGHOUT / Phase error: 31.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 7264 5 %From PDB ID 4RDQ
Rwork0.2176 ---
obs-145754 99.9 %-
Displacement parametersBiso mean: 101.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30640 0 55 10 30705
LS refinement shellResolution: 3.1→3.211 Å
RfactorNum. reflection% reflection
Rfree0.358 765 5.27 %
Rwork0.3344 13735 -
obs--99.9 %

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