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- PDB-5era: Human Connexin-26 (Calcium-free) -

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Basic information

Entry
Database: PDB / ID: 5era
TitleHuman Connexin-26 (Calcium-free)
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 / gap junction channel activity involved in cell communication by electrical coupling / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / gap junction ...Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / gap junction channel activity involved in cell communication by electrical coupling / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / gap junction / astrocyte projection / Gap junction assembly / gap junction channel activity / endoplasmic reticulum-Golgi intermediate compartment / inner ear development / decidualization / lateral plasma membrane / response to retinoic acid / cellular response to glucagon stimulus / cellular response to dexamethasone stimulus / response to ischemia / response to progesterone / sensory perception of sound / transmembrane transport / cell-cell signaling / response to estradiol / cellular response to oxidative stress / cell body / 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: 3.8 Å
AuthorsPurdy, M.D. / Bennett, B.C. / Baker, K.A. / Yeager, M.J.
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 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)52,2782
Polymers52,2782
Non-polymers00
Water00
1
B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein


Theoretical massNumber of molelcules
Total (without water)313,66612
Polymers313,66612
Non-polymers00
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
2
B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein

B: Gap junction beta-2 protein
A: Gap junction beta-2 protein


Theoretical massNumber of molelcules
Total (without water)156,8336
Polymers156,8336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13950 Å2
ΔGint-102 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.727, 155.727, 160.699
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
Source: (gene. exp.) Homo sapiens (human) / Gene: GJB2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P29033
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: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 15 mM Sodium formate, 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 7398 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 152.13 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.184 / Net I/av σ(I): 21.375 / Net I/σ(I): 5.9 / Num. measured all: 85071
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.3-3.3665600.85898.8
3.36-3.427.35670.86100
3.42-3.487.55790.917100
3.48-3.557.55640.917100
3.55-3.637.55740.925100
3.63-3.727.65641.5551000.642
3.72-3.817.55741.009100
3.81-3.917.45801.0041000.904
3.91-4.037.65770.9461000.62
4.03-4.167.55620.9441000.533
4.16-4.317.55690.9981000.316
4.31-4.487.55841.1231000.195
4.48-4.687.45771.1131000.138
4.68-4.937.65661.32199.80.105
4.93-5.247.55961.4231000.099
5.24-5.647.55691.36299.80.113
5.64-6.217.45841.2421000.085
6.21-7.17.45881.3121000.07
7.1-8.947.35981.5551000.041
8.94-506.86182.23298.90.037

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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: 5ER7

5er7


Resolution: 3.8→44.132 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3334 741 10.02 %
Rwork0.3005 6657 -
obs0.3037 7398 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.98 Å2 / Biso mean: 127.161 Å2 / Biso min: 58.25 Å2
Refinement stepCycle: final / Resolution: 3.8→44.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 0 0 2539
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052617
X-RAY DIFFRACTIONf_angle_d0.8193559
X-RAY DIFFRACTIONf_chiral_restr0.05419
X-RAY DIFFRACTIONf_plane_restr0.003427
X-RAY DIFFRACTIONf_dihedral_angle_d12.839893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8001-4.09330.36111480.278213301478100
4.0933-4.50490.32131480.24281331147999
4.5049-5.15590.25331480.20551328147699
5.1559-6.49250.36661490.35861338148798
6.4925-44.13450.35361480.33491330147894

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