[English] 日本語
Yorodumi
- PDB-28me: Connexin 26 from L Paradoxa in GDN detergent - hemichannel focuss... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 28me
TitleConnexin 26 from L Paradoxa in GDN detergent - hemichannel focussed conformation 2
ComponentsConnexin 26 from Lepidosiren paradoxa
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: 2.9 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)397,95748
Polymers374,21312
Non-polymers23,74436
Water5,621312
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 "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALYSLYSAA8 - 2238 - 223
d_12LMTLMTLMTLMTAM301
d_13PTYPTYPTYPTYAN302
d_14PTYPTYPTYPTYBP301
d_21ALAALALYSLYSBB8 - 2238 - 223
d_22LMTLMTLMTLMTBQ302
d_23PTYPTYPTYPTYBR303
d_24PTYPTYPTYPTYCS301
d_31ALAALALYSLYSCC8 - 2238 - 223
d_32LMTLMTLMTLMTCT302
d_33PTYPTYPTYPTYCU303
d_34PTYPTYPTYPTYDV301
d_41ALAALALYSLYSDD8 - 2238 - 223
d_42LMTLMTLMTLMTDW302
d_43PTYPTYPTYPTYDX303
d_44PTYPTYPTYPTYEY301
d_51ALAALALYSLYSEE8 - 2238 - 223
d_52LMTLMTLMTLMTEZ302
d_53PTYPTYPTYPTYEAA303
d_54PTYPTYPTYPTYFBA301
d_61ALAALALYSLYSFF8 - 2238 - 223
d_62LMTLMTLMTLMTFCA302
d_63PTYPTYPTYPTYFDA303
d_64PTYPTYPTYPTYAO303
d_71ALAALALYSLYSGG8 - 2238 - 223
d_72LMTLMTLMTLMTGEA301
d_73PTYPTYPTYPTYGFA302
d_74PTYPTYPTYPTYHHA301
d_81ALAALALYSLYSHH8 - 2238 - 223
d_82LMTLMTLMTLMTHIA302
d_83PTYPTYPTYPTYHJA303
d_84PTYPTYPTYPTYIKA301
d_91ALAALALYSLYSII8 - 2238 - 223
d_92LMTLMTLMTLMTILA302
d_93PTYPTYPTYPTYIMA303
d_94PTYPTYPTYPTYJNA301
d_101ALAALALYSLYSJJ8 - 2238 - 223
d_102LMTLMTLMTLMTJOA302
d_103PTYPTYPTYPTYJPA303
d_104PTYPTYPTYPTYKQA301
d_111ALAALALYSLYSKK8 - 2238 - 223
d_112LMTLMTLMTLMTKRA302
d_113PTYPTYPTYPTYKSA303
d_114PTYPTYPTYPTYLTA301
d_121ALAALALYSLYSLL8 - 2238 - 223
d_122LMTLMTLMTLMTLUA302
d_123PTYPTYPTYPTYLVA303
d_124PTYPTYPTYPTYGGA303

NCS oper:
IDCodeMatrixVector
1given(0.49995843032926, 0.86604938988802, 0.00014905467860778), (-0.86604832056147, 0.49995752613585, 0.0016668871521299), (0.0013690855927386, -0.00096246283819497, 0.99999859963398)-42.710833047362, 159.57286797668, -0.07017450422876
2given(-0.49050882006688, 0.8714355964647, -0.0010481654466188), (-0.87143538360148, -0.49050631735155, 0.0019811222977792), (0.0012122887180386, 0.0018851664187439, 0.99999748824866)72.572496854989, 275.60407332501, -0.44765266324751
3given(-0.99998494317389, 0.0053721083885762, -0.0011197664847584), (-0.0053735533064091, -0.99998472850863, 0.0012913846785717), (-0.0011128119257895, 0.0012973823593137, 0.99999853922325)233.21751288031, 234.2136592324, -0.13122852174637
4given(-0.4851197326698, -0.87444711517725, 0.0010429441830966), (0.87444579391886, -0.48511579518121, 0.0026867756351557), (-0.0018434945065779, 0.0022154060320714, 0.99999584674343)276.13756879405, 70.791292159837, -0.10590131940313
5given(0.51231173395771, -0.85879948622971, -0.0003601400193835), (0.85879757978239, 0.51230960564457, 0.0023632444248967), (-0.0018450499066293, -0.001520005226114, 0.99999714268339)157.43868519099, -43.976788204268, 0.36476413187943
6given(0.48852246724512, 0.87246394786861, 0.012347415367657), (0.87249637520103, -0.48860159272231, 0.004307998409619), (0.009791540114509, 0.008668521139427, -0.99991448758553)-43.417060210714, 71.652949957603, 231.39730166825
7given(-0.50061875550688, 0.86566779757059, 0.00035480137902773), (0.86560933971624, 0.50058009899577, 0.01183365900307), (0.010066411016952, 0.0062312710306405, -0.99992991685947)74.066759829482, -43.690707467897, 231.79254366393
8given(-0.99995030206796, -0.0019992751514411, -0.0097671025929335), (-0.0020616229266719, 0.99997753800546, 0.0063775540340262), (0.0097541327190212, 0.0063973731654119, -0.99993196294122)234.64773163385, -0.27277962484621, 231.71253165973
9given(-0.49559493322204, -0.86849508394358, -0.010097095149956), (-0.86851296489084, 0.49565085246835, -0.0039322085281145), (0.0084197375942384, 0.0068206754225675, -0.99994129147947)277.18126876388, 160.67835974509, 231.79130465828
10given(0.51245308608474, -0.85871450750302, -0.0011086776238347), (-0.85865901678783, -0.51240434509526, -0.012102892896221), (0.0098248384809771, 0.007154140853638, -0.99992614268128)157.53305622513, 278.37349064993, 231.70318230836
11given(0.99972035651378, 0.02056263514116, 0.011678476270794), (0.020655880471739, -0.99975526884155, -0.0079206707730494), (0.011512748320588, 0.0081596850190028, -0.99990043312647)-3.5952968189634, 232.1715582321, 231.27311240978

-
Components

#1: Protein
Connexin 26 from Lepidosiren paradoxa


Mass: 31184.395 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Connexin 26 from Lepidosiren paradoxa with added linker and His tag.
Source: (gene. exp.) Lepidosiren paradoxa (South American lungfish)
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.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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

-
Processing

EM software
IDNameVersionCategory
1RELION5particle selection
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10RELION5initial Euler assignment
13RELION53D reconstruction
14PHENIX2.0_5885model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1099552
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71467 / 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: 46.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421708
ELECTRON MICROSCOPYf_angle_d0.930129220
ELECTRON MICROSCOPYf_chiral_restr0.05423312
ELECTRON MICROSCOPYf_plane_restr0.01083396
ELECTRON MICROSCOPYf_dihedral_angle_d8.98733923
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints3.5231915056062E-13
ens_1d_3AAELECTRON MICROSCOPYNCS constraints6.1066321796078E-11
ens_1d_4AAELECTRON MICROSCOPYNCS constraints7.8063923176527E-13
ens_1d_5AAELECTRON MICROSCOPYNCS constraints3.5696205195187E-13
ens_1d_6AAELECTRON MICROSCOPYNCS constraints9.833336095858E-12
ens_1d_7AAELECTRON MICROSCOPYNCS constraints3.1041443143577E-13
ens_1d_8AAELECTRON MICROSCOPYNCS constraints3.0729746619906E-13
ens_1d_9AAELECTRON MICROSCOPYNCS constraints1.8003468456771E-13
ens_1d_10AAELECTRON MICROSCOPYNCS constraints4.8726270908138E-13
ens_1d_11AAELECTRON MICROSCOPYNCS constraints9.532270906703E-11
ens_1d_12AAELECTRON MICROSCOPYNCS constraints1.0408567628454E-11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more