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- PDB-2zw3: Structure of the connexin-26 gap junction channel at 3.5 angstrom... -

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Basic information

Entry
Database: PDB / ID: 2zw3
TitleStructure of the connexin-26 gap junction channel at 3.5 angstrom resolution
ComponentsGap junction beta-2 protein
KeywordsCELL ADHESION / ION CHANNEL / alpha helical membrane channel / two double layered lipid spanning / cellular adhesion / Cell junction / Cell membrane / Deafness / Disease mutation / Ectodermal dysplasia / Gap junction / Hearing / Ichthyosis / Membrane / Non-syndromic deafness / Palmoplantar keratoderma / Polymorphism / Transmembrane
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 channel protein cysteine-rich domain / Gap junction beta-2 protein (Cx26) / de novo design (two linked rop proteins) / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. ...Gap junction channel protein cysteine-rich domain / Gap junction beta-2 protein (Cx26) / de novo design (two linked rop proteins) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Gap junction beta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsMaeda, S. / Nakagawa, S. / Suga, M. / Yamashita, E. / Oshima, A. / Fujiyoshi, Y. / Tsukihara, T.
CitationJournal: Nature / Year: 2009
Title: Structure of the connexin 26 gap junction channel at 3.5 A resolution
Authors: Maeda, S. / Nakagawa, S. / Suga, M. / Yamashita, E. / Oshima, A. / Fujiyoshi, Y. / Tsukihara, T.
History
DepositionDec 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gap junction beta-2 protein
B: Gap junction beta-2 protein
C: Gap junction beta-2 protein
D: Gap junction beta-2 protein
E: Gap junction beta-2 protein
F: Gap junction beta-2 protein


Theoretical massNumber of molelcules
Total (without water)157,4826
Polymers157,4826
Non-polymers00
Water00
1
A: Gap junction beta-2 protein
B: Gap junction beta-2 protein
C: Gap junction beta-2 protein
D: Gap junction beta-2 protein
E: Gap junction beta-2 protein
F: Gap junction beta-2 protein

A: Gap junction beta-2 protein
B: Gap junction beta-2 protein
C: Gap junction beta-2 protein
D: Gap junction beta-2 protein
E: Gap junction beta-2 protein
F: Gap junction beta-2 protein


Theoretical massNumber of molelcules
Total (without water)314,96512
Polymers314,96512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area45230 Å2
ΔGint-220 kcal/mol
Surface area111280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.617, 111.245, 155.387
Angle α, β, γ (deg.)90.00, 114.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
131A
141B
151C
161D
171E
181F
191A
201B
211C
221D
231E
241F
12A
22D
13B
23E
14C
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSILEILE1AA15 - 3315 - 33
211LYSLYSILEILE1BB15 - 3315 - 33
311LYSLYSILEILE1CC15 - 3315 - 33
411LYSLYSILEILE1DD15 - 3315 - 33
511LYSLYSILEILE1EE15 - 3315 - 33
611LYSLYSILEILE1FF15 - 3315 - 33
721METMETMETMET2AA3434
821METMETMETMET2BB3434
921METMETMETMET2CC3434
1021METMETMETMET2DD3434
1121METMETMETMET2EE3434
1221METMETMETMET2FF3434
1331ILEILEGLYGLY1AA35 - 10935 - 109
1431ILEILEGLYGLY1BB35 - 10935 - 109
1531ILEILEGLYGLY1CC35 - 10935 - 109
1631ILEILEGLYGLY1DD35 - 10935 - 109
1731ILEILEGLYGLY1EE35 - 10935 - 109
1831ILEILEGLYGLY1FF35 - 10935 - 109
1941LYSLYSTYRTYR1AA125 - 217125 - 217
2041LYSLYSTYRTYR1BB125 - 217125 - 217
2141LYSLYSTYRTYR1CC125 - 217125 - 217
2241LYSLYSTYRTYR1DD125 - 217125 - 217
2341LYSLYSTYRTYR1EE125 - 217125 - 217
2441LYSLYSTYRTYR1FF125 - 217125 - 217
112ASPASPASNASN1AA2 - 142 - 14
212ASPASPASNASN1DD2 - 142 - 14
113ASPASPASNASN1BB2 - 142 - 14
213ASPASPASNASN1EE2 - 142 - 14
114ASPASPASNASN1CC2 - 142 - 14
214ASPASPASNASN1FF2 - 142 - 14

NCS ensembles :
ID
1
2
3
4
DetailsTHE GAP JUNCTION CHANNEL FUNCTIONS AS AN INTERCELLULAR CHANNEL IN DODECAMERIC STATE. ALTHOUGH THIS STRUCTURE HAS SIX SUBUNITS IN THE ASYMMETRIC UNIT, IT FORMS HOMO-DODECAMERWITH THE ANOTHER HEXAMER RELATED BY CRYSTALLOGRAPHIC TWO-FOLD.

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Components

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


Mass: 26247.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Plasmid: pBlueBac4.5 / 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: 11

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-18% PEG 200, 0.1M Sodium phosphate, 0.1M Sodium chloride, 0.01M DTT , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 17, 2007
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→141 Å / Num. all: 33085 / Num. obs: 31138 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 93.594 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 26.1
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3266 / Rsym value: 0.378 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3.5→22 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.823 / SU B: 39.893 / SU ML: 0.619 / Cross valid method: THROUGHOUT / ESU R Free: 0.735 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35123 1565 5 %RANDOM
Rwork0.3368 ---
obs0.33755 29595 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 137.197 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å22.23 Å2
2--1.57 Å20 Å2
3----3.49 Å2
Refinement stepCycle: LAST / Resolution: 3.5→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9834 0 0 0 9834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210186
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.92813794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11851194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02522420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.837151680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6721560
X-RAY DIFFRACTIONr_chiral_restr0.1060.21560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027482
X-RAY DIFFRACTIONr_nbd_refined0.2890.25815
X-RAY DIFFRACTIONr_nbtor_refined0.3290.26873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2424
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3640.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.220
X-RAY DIFFRACTIONr_mcbond_it2.7171.56176
X-RAY DIFFRACTIONr_mcangle_it5.43429774
X-RAY DIFFRACTIONr_scbond_it6.16134737
X-RAY DIFFRACTIONr_scangle_it9.0884.54020
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1540tight positional0.020.05
12B1540tight positional0.020.05
13C1540tight positional0.020.05
14D1540tight positional0.020.05
15E1540tight positional0.020.05
16F1540tight positional0.030.05
21A96tight positional0.030.05
31B96tight positional0.020.05
41C96tight positional0.030.05
11A4medium positional0.510.5
12B4medium positional0.560.5
13C4medium positional0.340.5
14D4medium positional0.410.5
15E4medium positional0.720.5
16F4medium positional0.720.5
11A1540tight thermal0.090.5
12B1540tight thermal0.040.5
13C1540tight thermal0.050.5
14D1540tight thermal0.090.5
15E1540tight thermal0.040.5
16F1540tight thermal0.050.5
21A96tight thermal1.750.5
31B96tight thermal2.30.5
41C96tight thermal1.740.5
11A4medium thermal0.1850
12B4medium thermal0.150
13C4medium thermal0.2850
14D4medium thermal0.5850
15E4medium thermal1.0850
16F4medium thermal0.2950
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 131 -
Rwork0.49 2142 -
obs--95.06 %

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