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- PDB-28mc: Connexin 26 from L Paradoxa in GDN detergent - hemichannel focuss... -

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Basic information

Entry
Database: PDB / ID: 28mc
TitleConnexin 26 from L Paradoxa in GDN detergent - hemichannel focussed conformation 1
ComponentsConnexin 26
KeywordsMEMBRANE PROTEIN / Connexin / Gap Junction Channel / Ion Channel
Function / homologyPHOSPHATIDYLETHANOLAMINE
Function and homology information
Biological speciesLepidosiren paradoxa (South American lungfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBrotherton, D.H. / Cameron, A.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P010393/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of Connexin 26 from L Paradoxa
Authors: Brotherton, D.H. / Dale, N. / Cameron, A.D.
History
DepositionFeb 6, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Connexin 26
B: Connexin 26
C: Connexin 26
D: Connexin 26
E: Connexin 26
F: Connexin 26
G: Connexin 26
H: Connexin 26
I: Connexin 26
J: Connexin 26
K: Connexin 26
L: Connexin 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,95748
Polymers374,21312
Non-polymers23,74436
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "E"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "F"
d_1ens_2chain "L"
d_2ens_2chain "H"
d_3ens_2chain "I"
d_4ens_2chain "J"
d_5ens_2chain "K"
d_6ens_2chain "G"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1TRPTRPGLNGLNEE3 - 2243 - 224
d_12ens_1LMTLMTLMTLMTEZ302
d_13ens_1PTYPTYPTYPTYEAA303
d_14ens_1PTYPTYPTYPTYFBA301
d_21ens_1TRPTRPGLNGLNBB3 - 2243 - 224
d_22ens_1LMTLMTLMTLMTBQ302
d_23ens_1PTYPTYPTYPTYBR303
d_24ens_1PTYPTYPTYPTYCS301
d_31ens_1TRPTRPGLNGLNCC3 - 2243 - 224
d_32ens_1LMTLMTLMTLMTCT302
d_33ens_1PTYPTYPTYPTYCU303
d_34ens_1PTYPTYPTYPTYDV301
d_41ens_1TRPTRPGLNGLNDD3 - 2243 - 224
d_42ens_1LMTLMTLMTLMTDW302
d_43ens_1PTYPTYPTYPTYDX303
d_44ens_1PTYPTYPTYPTYEY301
d_51ens_1TRPTRPGLNGLNAA3 - 2243 - 224
d_52ens_1LMTLMTLMTLMTAM301
d_53ens_1PTYPTYPTYPTYAN302
d_54ens_1PTYPTYPTYPTYBP301
d_61ens_1TRPTRPGLNGLNFF3 - 2243 - 224
d_62ens_1LMTLMTLMTLMTFCA302
d_63ens_1PTYPTYPTYPTYFDA303
d_64ens_1PTYPTYPTYPTYAO303
d_11ens_2THRTHRGLNGLNLL5 - 2245 - 224
d_12ens_2LMTLMTLMTLMTLUA302
d_13ens_2PTYPTYPTYPTYLVA303
d_14ens_2PTYPTYPTYPTYGGA303
d_21ens_2THRTHRGLNGLNHH5 - 2245 - 224
d_22ens_2LMTLMTLMTLMTHIA302
d_23ens_2PTYPTYPTYPTYHJA303
d_24ens_2PTYPTYPTYPTYIKA301
d_31ens_2THRTHRGLNGLNII5 - 2245 - 224
d_32ens_2LMTLMTLMTLMTILA302
d_33ens_2PTYPTYPTYPTYIMA303
d_34ens_2PTYPTYPTYPTYJNA301
d_41ens_2THRTHRGLNGLNJJ5 - 2245 - 224
d_42ens_2LMTLMTLMTLMTJOA302
d_43ens_2PTYPTYPTYPTYJPA303
d_44ens_2PTYPTYPTYPTYKQA301
d_51ens_2THRTHRGLNGLNKK5 - 2245 - 224
d_52ens_2LMTLMTLMTLMTKRA302
d_53ens_2PTYPTYPTYPTYKSA303
d_54ens_2PTYPTYPTYPTYLTA301
d_61ens_2THRTHRGLNGLNGG5 - 2245 - 224
d_62ens_2LMTLMTLMTLMTGEA301
d_63ens_2PTYPTYPTYPTYGFA302
d_64ens_2PTYPTYPTYPTYHHA301

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.99991095261272, 0.013343673950852, 0.00018223779618125), (-0.013342996957919, -0.99990548560398, 0.00331425576148), (0.00022644492035693, 0.0033115290373036, 0.99999449123389)232.47243933361, 234.87502963073, -0.3861107598527
2given(-0.51698365386723, -0.85598946704678, 0.0031518151991551), (0.85599339498703, -0.51698672314668, -0.00018928456685132), (0.0017914722072743, 0.002600075965705, 0.99999501510373)277.02966369296, 76.898832051078, -0.37417881868544
3given(0.49807044727732, -0.86713581714451, -0.0011420044185823), (0.86713041950564, 0.49807144301055, -0.0031101809228371), (0.0032657490646793, 0.00055882243278827, 0.9999945112852)160.14192028842, -42.429968000032, -0.37686661697522
4given(-0.49453558215444, 0.86915551827591, -0.0018008424966708), (-0.869153614203, -0.49452627343153, 0.0039698619339147), (0.0025598634777397, 0.003528446747153, 0.99999049853612)73.374492444603, 276.03317150154, -0.6661515416598
5given(0.496505199241, 0.86803277121744, -0.0013020058469594), (-0.8680325826043, 0.49650643184232, 0.00089368703743345), (0.0014222039130161, 0.00068646323732204, 0.99999875305135)-42.576576440859, 160.1216604273, -0.20417785279241
6given(-0.49138555094477, -0.87094213009992, -0.00021526661838069), (0.87094148419502, -0.49138484935203, -0.0013641610810685), (0.0010823266029017, -0.00085781367250837, 0.99999904636196)276.09642696248, 72.925759094528, -0.10769614958787
7given(-0.9996363101455, -0.026744130240987, -0.0034639480868475), (0.026740956908529, -0.99964193646632, 0.0009592087765111), (-0.0034883609778024, 0.00086623063548696, 0.99999354047023)236.85500744199, 230.84124877046, 0.30645615898192
8given(-0.50598442689969, 0.86254137682501, -0.0014604793070546), (-0.86254238610051, -0.5059847972344, 0.00013094925338489), (-0.00062603117673627, 0.0013259835892842, 0.99999892492567)75.345033096372, 276.81175397152, -0.058173800074968
9given(0.49883953476997, 0.86668978104971, -0.0028181508975499), (-0.86669383565103, 0.49884018062027, -0.00051907922380321), (0.0009559262439235, 0.0027014112493516, 0.99999589428271)-42.38309337975, 159.99257821815, -0.44341713661632
10given(0.4989121803355, -0.86665191086715, -0.0010496205007686), (0.86664994206045, 0.49891328429508, -0.0018473441790895), (0.0021246739741392, 1.2008966043115E-5, 0.9999977428056)159.94701463111, -42.483066777883, -0.27409606317499

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Components

#1: Protein
Connexin 26


Mass: 31184.395 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Connexin 26 from Lepidosiren paradoxa with additional linker and His tag.
Source: (gene. exp.) Lepidosiren paradoxa (South American lungfish)
Plasmid: pfastbac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical...
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dodecameric gap junction channel for Connexin 26 / Type: COMPLEX / Details: Classification was focussed on chains A-F / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Lepidosiren paradoxa (South American lungfish)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 46.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12277

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX2.0_5885model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1099552
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57156 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00521366
ELECTRON MICROSCOPYf_angle_d0.991128788
ELECTRON MICROSCOPYf_chiral_restr0.05943222
ELECTRON MICROSCOPYf_plane_restr0.01733342
ELECTRON MICROSCOPYf_dihedral_angle_d11.6754014
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EEELECTRON MICROSCOPYNCS constraints3.4950449001459E-13
ens_1d_3EEELECTRON MICROSCOPYNCS constraints2.9165196158833E-11
ens_1d_4EEELECTRON MICROSCOPYNCS constraints2.780990388634E-13
ens_1d_5EEELECTRON MICROSCOPYNCS constraints1.3319305345803E-13
ens_1d_6EEELECTRON MICROSCOPYNCS constraints1.3612047153647E-10
ens_2d_2LLELECTRON MICROSCOPYNCS constraints3.9787301974301E-13
ens_2d_3LLELECTRON MICROSCOPYNCS constraints3.1834701985611E-13
ens_2d_4LLELECTRON MICROSCOPYNCS constraints3.2778514946899E-13
ens_2d_5LLELECTRON MICROSCOPYNCS constraints2.5432990813612E-11
ens_2d_6LLELECTRON MICROSCOPYNCS constraints2.2388015928859E-13

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