[English] 日本語
Yorodumi
- PDB-5era: Human Connexin-26 (Calcium-free) -

+
Open data


ID or keywords:

Loading...

-
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 / gap junction-mediated intercellular transport / 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 / Gap junction assembly / gap junction channel activity ...Transport of connexons to the plasma membrane / gap junction-mediated intercellular transport / 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 / Gap junction assembly / gap junction channel activity / endoplasmic reticulum-Golgi intermediate compartment / sensory perception of sound / transmembrane transport / cell-cell signaling / calcium ion binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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))

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
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