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- PDB-5er7: Connexin-26 Bound to Calcium -

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Basic information

Entry
Database: PDB / ID: 5er7
TitleConnexin-26 Bound to Calcium
ComponentsGap junction beta-2 protein
KeywordsCALCIUM BINDING PROTEIN / gap junction / ion channel / calcium binding / electrostatic gating
Function / homology
Function and homology information


Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly ...Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / astrocyte projection / gap junction channel activity / gap junction / cellular response to glucagon stimulus / inner ear development / decidualization / endoplasmic reticulum-Golgi intermediate compartment / lateral plasma membrane / response to retinoic acid / cellular response to dexamethasone stimulus / response to progesterone / response to ischemia / sensory perception of sound / transmembrane transport / response to estradiol / cell-cell signaling / cell body / cellular response to oxidative stress / response to lipopolysaccharide / calcium ion binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane
Similarity search - Function
Gap junction beta-2 protein (Cx26) / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction beta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.286 Å
AuthorsPurdy, M.D. / Bennett, B.C. / Baker, K.A. / Yeager, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1 HL048908 United States
Citation
Journal: Nat Commun / Year: 2016
Title: An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels.
Authors: Bennett, B.C. / Purdy, M.D. / Baker, K.A. / Acharya, C. / McIntire, W.E. / Stevens, R.C. / Zhang, Q. / Harris, A.L. / Abagyan, R. / Yeager, M.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins.
Authors: Lee, S.C. / Bennett, B.C. / Hong, W.X. / Fu, Y. / Baker, K.A. / Marcoux, J. / Robinson, C.V. / Ward, A.B. / Halpert, J.R. / Stevens, R.C. / Stout, C.D. / Yeager, M.J. / Zhang, Q.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Gap junction beta-2 protein
A: Gap junction beta-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3584
Polymers52,2782
Non-polymers802
Water0
1
B: Gap junction beta-2 protein
A: Gap junction beta-2 protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)314,14724
Polymers313,66612
Non-polymers48112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area36640 Å2
ΔGint-341 kcal/mol
Surface area76390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.092, 156.092, 160.077
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: D6 (2x6 fold dihedral))

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Components

#1: Protein Gap junction beta-2 protein / Connexin-26 / Cx26


Mass: 26138.848 Da / Num. of mol.: 2 / Fragment: full length protein / Mutation: C211S, C218S
Source method: isolated from a genetically manipulated source
Details: Due to a lack of electron density, we could not model residues 1-18, 96-133, and 217-226 in chain A and residues 1-20, 96-133, and 214-226 in chain B.
Source: (gene. exp.) Homo sapiens (human) / Gene: GJB2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P29033
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 15 mM Sodium formate, 20 mM CaCl2, 14% (w/v) PEG 3350
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→40 Å / Num. obs: 11481 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 140.58 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.175 / Net I/av σ(I): 13.447 / Net I/σ(I): 5.4 / Num. measured all: 105396
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.84-2.894.68650.81198.9
2.89-2.945.88970.807100
2.94-35.99110.811100
3-3.0668870.839100
3.06-3.1368890.835100
3.13-3.25.99140.894100
3.2-3.2868840.88100
3.28-3.3768920.889100
3.37-3.4768850.903100
3.47-3.5869200.906100
3.58-3.7168900.9261000.816
3.71-3.8569020.9841000.654
3.85-4.0369141.0681000.37
4.03-4.245.99091.1161000.246
4.24-4.515.98931.3151000.138
4.51-4.855.99131.4551000.087
4.85-5.345.99141.63799.80.077
5.34-6.115.89152.0499.80.086
6.11-7.695.89202.11499.70.055
7.69-405.39582.26498.80.036

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PolyAla build from a cryoEM map

Resolution: 3.286→34.427 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3184 549 4.78 %Random
Rwork0.2789 10932 --
obs0.2807 11481 98.94 %-
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.63 Å2 / Biso mean: 131.4073 Å2 / Biso min: 76.6 Å2
Refinement stepCycle: final / Resolution: 3.286→34.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 2 0 2549
Biso mean--135.8 --
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042627
X-RAY DIFFRACTIONf_angle_d0.713569
X-RAY DIFFRACTIONf_chiral_restr0.03419
X-RAY DIFFRACTIONf_plane_restr0.003428
X-RAY DIFFRACTIONf_dihedral_angle_d13.305900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.286-3.61630.39161230.30452645276897
3.6163-4.13890.30191500.258327282878100
4.1389-5.21160.27111440.254527422886100
5.2116-34.42860.34171320.29392817294999

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