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electron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state

by electron crystallography, at 1.9 A resolution

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Orientation:

#1: Biological unit as octameric, Image by Jmol

#2: Biological unit as octameric, Image by Jmol

#3: Depositted structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2b6o
Titleelectron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state
DescriptorLens fiber major intrinsic protein
Keywordsmembrane protein, aquaporin-0 junctions, AQP0, lens MIP, lipid-protein interactions, membrane, lipid bilayer, closed water pore, electron crystallography
AuthorsGonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S.C., Walz, T.
DateDeposition: 2005-10-03, Release: 2005-12-06
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Biological unit as octameric, Image by Jmol

#2: Biological unit as octameric, Image by Jmol

#3: Depositted structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleNature, Vol. 438, Issue 7068, Page 633-8, Year 2005
TitleLipid-protein interactions in double-layered two-dimensional AQP0 crystals.
AuthorsTamir Gonen, Yifan Cheng, Piotr Sliz, Yoko Hiroaki, Yoshinori Fujiyoshi, Stephen C Harrison, Thomas Walz
Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.
KeywordsAnimals, Aquaporins (chemistry), Crystallization, Crystallography, Hydrogen Bonding, Lens, Crystalline (chemistry), Lipid Bilayers (chemistry), Membrane Lipids (metabolism), Models, Molecular, Protein Binding, Protein Structure, Quaternary, Sheep, Water (analysis)
LinksDOI: 10.1038/nature04321, PubMed: 16319884, PMC: PMC1350984
Components
ID 1 : Aquaporin-0
Image
DescriptionLens fiber major intrinsic protein
Typepolypeptide(L)
Formula weight28285.104 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Common name: sheep
Genus: Ovis
NCBI taxonomy: ID:9940
Organism scientific: Ovis aries

LinksUniProt: Q6J8I9, Sequence view
ID 2 : 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Image
Description1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Typenon-polymer
Formula weight677.940 Da
Number of molecules9
ID2
SourceMethod: Obtained synthetically
ID 3 : water
Image
Descriptionwater
Typewater
Formula weight18.015 Da
Number of molecules79
ID3
SourceMethod: Isolated from a natural source
Sample
Experiment
MethodELECTRON CRYSTALLOGRAPHY
Crystals number286
Crystal
Density Matthews3.03
Density percent sol59.44
Crystal grow
MethodMICRODIALYSIS
PH6
Details20mM MES pH 6.0, 50mM MgCl2, 5mM DTT, MICRODIALYSIS, temperature 300K
Temp300 Kelvin
Electron Microscopy
Diffraction
Ambient temp281
electron source
electron sourceELECTRON MICROSCOPE
TypeJEM3000SFF
Detector
Details4k X 4k
DetectorCCD
Collection date2003-12-01
TypeGATAN
Processing
Reflection
Ordinal1
B iso Wilson estimate18.1
D resolution high1.9
D resolution low20
Rmerge I obs0.166
Redundancy5.7
Percent possible obs80
Reflection shell
Ordinal1
D res high1.9
D res low2.0
Redundancy2.5
Percent possible all70.5
2D projection selection
Software nameCNS 1.1
Computing
Data reduction dsGATAN
Data reduction iiGATAN
Structure refinementCNS 1.1
Structure solutionCNS
Refine
Refine idELECTRON CRYSTALLOGRAPHY
B iso mean58.4
Aniso B11-7.32
Aniso B120.00
Aniso B130.00
Aniso B22-7.32
Aniso B230.00
Aniso B3314.64
Ls R factor R free0.299
Ls R factor R free error0.008
Ls R factor R work0.258
Ls d res high1.90 A
Ls d res low5.00 A
Ls number reflection R free1580
Ls number reflection all16180
Ls number reflection obs14600
Ls percent reflection R free9.8
R Free selection detailsRANDOM
Data cutoff high absF2606056.45
Data cutoff low absF0.000000
Isotropic thermal modelRESTRAINED
Ls cross valid methodTHROUGHOUT
Ls sigma F0.0
Method to determine structMOLECULAR REPLACEMENT
Starting model1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography
Stereochemistry target valuesEngh & Huber
Refine hist
Cycle idLAST
Refine idELECTRON CRYSTALLOGRAPHY
D res high1.90
D res low5.00
Solvent atoms79
Total atoms2211
Ligand atoms349
Protein atoms1783
Software
Ordinal1
Classificationdata collection
NameGATAN
Software
Ordinal2
Classificationdata reduction
NameGATAN
Software
Ordinal3
Classificationmodel building
NameCNS
Software
Ordinal4
Classificationrefinement
NameCNS
Version1.1
Download
PDB format
Allpdb2b6o.ent.gz
pdb2b6o.ent (uncompressed file)
Header onlypdb2b6o.ent.gz
mmCIF format
mmCIF2b6o.cif.gz
XML format
All2b6o.xml.gz
No-atom2b6o-noatom.xml.gz
Ext-atom2b6o-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB