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STRUCTURE OF ACETYLCHOLINE RECEPTOR PORE FROM ELECTRON IMAGES
by electron microscopy, at 4.0 A resolution
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Entry
Database / IDPORTEIN DATA BANK (PDB) / 1oed
TitleSTRUCTURE OF ACETYLCHOLINE RECEPTOR PORE FROM ELECTRON IMAGES
DescriptorACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN, ACETYLCHOLINE RECEPTOR PROTEIN, BETA CHAIN, ACETYLCHOLINE RECEPTOR PROTEIN, DELTA CHAIN, ACETYLCHOLINE RECEPTOR PROTEIN, GAMMA CHAIN
AuthorsMiyazawa, A., Fujiyoshi, Y., Unwin, N.
Images
image
image
image
KeywordsION CHANNEL/RECEPTOR, ION CHANNEL/RECEPTOR, ION CHANNEL, TUBULAR CRYSTAL, ACETYLCHOLINE RECEPTOR, TRANSMEMBRANE,
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Cite: data citing same article

Fit: target map of fitting

Deposition2003-03-24
Release2003-06-26
PDBj Mine pagesSummaryStructural DetailsExperimental DetailsFunctional Details
Other databasesRCSB-PDBPDBeCATHCEFSSPSCOPVAST
Article
Citation - primary
ArticleNature, Vol. 423, Issue 6943, Page 949-55, Year 2003
TitleStructure and gating mechanism of the acetylcholine receptor pore.
AuthorsAtsuo Miyazawa, Yoshinori Fujiyoshi, Nigel Unwin
AffiliationRIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.
ChemicalsIons, Receptors, Cholinergic, Acetylcholine (51-84-3)
KeywordsAcetylcholine, Amino Acid Sequence, Animals, Crystallization, Electric Conductivity, Ion Channel Gating, Ions, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Receptors, Cholinergic, Torpedo
LinksPubMed: 12827192 DOI: 10.1038/nature01748
Citation - 1
ArticleJ. Mol. Biol., Vol. 319, Issue 5, Page 1165-76, Year 2002
TitleActivation of the nicotinic acetylcholine receptor involves a switch in conformation of the alpha subunits.
AuthorsN Unwin, A Miyazawa, J Li, Y Fujiyoshi
AffiliationMRC Laboratory of Molecular Biology, Neurobiology Division, Hills Road, Cambridge CB2 2QH, UK.
ChemicalsAChBP protein, Lymnaea, Carrier Proteins, Protein Subunits, Receptors, Nicotinic, Acetylcholine (51-84-3)
KeywordsAcetylcholine, Animals, Binding Sites, Carrier Proteins, Microscopy, Electron, Models, Molecular, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits, Receptors, Nicotinic, Torpedo
LinksPubMed: 12079355 DOI: 10.1016/S0022-2836(02)00381-9
Citation - 2
ArticleJ. Mol. Biol., Vol. 229, Issue 4, Page 1101-24, Year 1993
TitleNicotinic acetylcholine receptor at 9 A resolution.
AuthorsN Unwin
AffiliationMRC Laboratory of Molecular Biology, Cambridge, U.K.
ChemicalsReceptors, Nicotinic
KeywordsAmino Acid Sequence, Animals, Cell Membrane, Fourier Analysis, Image Processing, Computer-Assisted, Microscopy, Electron, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Receptors, Nicotinic, Sequence Homology, Amino Acid, Torpedo, X-Ray Diffraction
LinksPubMed: 8445638
Citation - 3
ArticleJ. Mol. Biol., Vol. 288, Issue 4, Page 765-86, Year 1999
TitleNicotinic acetylcholine receptor at 4.6 A resolution: transverse tunnels in the channel wall.
AuthorsA Miyazawa, Y Fujiyoshi, M Stowell, N Unwin
AffiliationMRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.
ChemicalsMuscle Proteins, Receptors, Nicotinic, peripheral membrane protein 43K
KeywordsAnimals, Fourier Analysis, Microscopy, Electron, Muscle Proteins, Protein Conformation, Receptors, Nicotinic, Torpedo
LinksPubMed: 10329178
Components
ID 1 : NICOTINIC ACETYLCHOLINE RECEPTOR
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DescriptionACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
Typepolypeptide(L)
FragmentMEMBRANE-SPANNING DOMAIN, RESIDUES 235-461
Formula weight25389.121 Da
Number of molecules2.
SequencePLYFVVNVII PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF TMIFVISSII ITVVVINTHH RSPSTHTMPQ WVRKIFIDTI PNVMFFSTMK RASKEKQENK IFADDIDISD ISGKQVTGEV IFQTPLIKNP DVKSAIEGVK YIAEHMKSDE ESSNAAEEWK YVAMVIDHIL LCVFMLICII GTVSVFAGRL IELSQEG
SourceMethod: Isolated from a natural source
Common name: MARBLED ELECTRIC RAY
NCBI_taxonomy: ID:7788
Organ: ELECTRIC ORGAN
Organism scientific: TORPEDO MARMORATA
Tissue: DERIVED FROM MUSCLE
LinksUniProt: ACHA_TORCA
ID 2 : NICOTINIC ACETYLCHOLINE RECEPTOR
Viewer control
DescriptionACETYLCHOLINE RECEPTOR PROTEIN, BETA CHAIN
Typepolypeptide(L)
FragmentMEMBRANE-SPANNING DOMAIN, RESIDUES 241-490
Formula weight28387.535 Da
Number of molecules1.
SequencePLFYIVYTII PCILISILAI LVFYLPPDAG EKMSLSISAL LAVTVFLLLL ADKVPETSLS VPIIIRYLMF IMILVAFSVI LSVVVLNLHH RSPNTHTMPN WIRQIFIETL PPFLWIQRPV TTPSPDSKPT IISRANDEYF IRKPAGDFVC PVDNARVAVQ PERLFSEMKW HLNGLTQPVT LPQDLKEAVE AIKYIAEQLE SASEFDDLKK DWQYVAMVAD RLFLYVFFVI CSIGTFSIFL DASHNVPPDN
SourceMethod: Isolated from a natural source
Common name: MARBLED ELECTRIC RAY
NCBI_taxonomy: ID:7788
Organ: ELECTRIC ORGAN
Organism scientific: TORPEDO MARMORATA
Tissue: DERIVED FROM MUSCLE
LinksUniProt: ACHB_TORCA
ID 3 : NICOTINIC ACETYLCHOLINE RECEPTOR
Viewer control
DescriptionACETYLCHOLINE RECEPTOR PROTEIN, DELTA CHAIN
Typepolypeptide(L)
FragmentMEMBRANE-SPANNING DOMAIN, RESIDUES 246-505
Formula weight29371.305 Da
Number of molecules1.
SequencePLFYVINFIT PCVLISFLAS LAFYLPAESG EKMSTAISVL LAQAVFLLLT SQRLPETALA VPLIGKYLMF IMSLVTGVIV NCGIVLNFHF RTPSTHVLST RVKQIFLEKL PRILHMSRAD ESEQPDWQND LKLRRSSSVG YISKAQEYFN IKSRSELMFE KQSERHGLVP RVTPRIGFGN NNENIAASDQ LHDEIKSGID STNYIVKQIK EKNAYDEEVG NWNLVGQTID RLSMFIITPV MVLGTIFIFV MGNFNHPPAK
SourceMethod: Isolated from a natural source
Common name: MARBLED ELECTRIC RAY
NCBI_taxonomy: ID:7788
Organ: ELECTRIC ORGAN
Organism scientific: TORPEDO MARMORATA
Tissue: DERIVED FROM MUSCLE
LinksUniProt: ACHD_TORCA
ID 4 : NICOTINIC ACETYLCHOLINE RECEPTOR
Viewer control
DescriptionACETYLCHOLINE RECEPTOR PROTEIN, GAMMA CHAIN
Typepolypeptide(L)
FragmentMEMBRANE-SPANNING DOMAIN, RESIDUES 236-495
Formula weight29321.812 Da
Number of molecules1.
SequencePLFYIINIIA PCVLISSLVV LVYFLPAQAG GQKCTLSISV LLAQTIFLFL IAQKVPETSL NVPLIGKYLI FVMFVSMLIV MNCVIVLNVS LRTPNTHSLS EKIKHLFLGF LPKYLGMQLE PSEETPEKPQ PRRRSSFGIM IKAEEYILKK PRSELMFEEQ KDRHGLKRVN KMTSDIDIGT TVDLYKDLAN FAPEIKSCVE ACNFIAKSTK EQNDSGSENE NWVLIGKVID KACFWIALLL FSIGTLAIFL TGHFNQVPEF
SourceMethod: Isolated from a natural source
Common name: MARBLED ELECTRIC RAY
NCBI_taxonomy: ID:7788
Organ: ELECTRIC ORGAN
Organism scientific: TORPEDO MARMORATA
Tissue: DERIVED FROM MUSCLE
LinksUniProt: ACHG_TORCA
Sample
Assembly
Aggregation stateFILAMENT
NamePOSTSYNAPTIC MEMBRANE
Buffer
NameSODIUM CACODYLATE
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH6.8
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsLIQUID ETHANE
Assembly
Method detailsPQS
Oligomeric count5
Oligomeric detailspentameric
Electron Microscopy
Imaging
Accelerating voltage300 kV
Calibrated magnification36800 X
Date2002-10-01
DetailsTHE SPECIMENS WERE TUBULAR CRYSTALS GROWN IN LOW SALT BUFFER FROM ISOLATED TORPEDO POSTSYNAPTIC MEMBRANES. THEY WERE APPLIED TO THE THE MICROSCOPE GRIDS AND FROZEN IN THE SAME SOLUTION. THESE CRYSTALS WERE TOO SMALL AND DISTORTED TO YIELD MEANINGFUL ELECTRON DIFFRACTION PATTERNS, SO BOTH THE AMPLITUDE AND THE PHASE TERMS HAD TO BE MEASURED FROM FOURIER TRANSFORMS OF THE IMAGES. THE IMAGES WERE RECORDED USING A DOSE OF 2000 ELECTRONS/NM2 DURING THE PERIOD: JAN-1996 TO OCT-2002. THE DATASETS INVOLVED 4 HELICAL FAMILIES OF TUBES, WHICH WERE ANALYSED (INCLUDING CORRECTIONS FOR DISTORTIONS) AS DESCRIBED IN THE REFERENCES. STRUCTURES WERE SYNTHESISED FROM THE AMPLITUDE AND PHASE TERMS DERIVED FROM EACH HELICAL FAMILY. THE FINAL DATASET WAS OBTAINED BY AVERAGING THESE 4 STRUCTURES IN REAL SPACE.
Electron sourceFEG
Illumination modeLOW DOSE
Microscope modelJEOL JEM 300SFF
ModeBRIGHT FIELD
Nominal Cs1.3 mm
Nominal defocus max1800. nm
Nominal defocus min800. nm
Nominal magnification40000 X
Temperature4.2 Kelvin
Detector
TypeKODAK SO-163 FILM
Image scans
Number digital images359
Processing
3D reconstruction
DetailsNO REFINEMENT WAS CARRIED OUT ON THE MODEL. THE COORDINATES ARE PRELIMINARY. INCLUDED ARE ALL RESIDUES IN THE TRANSMEMBRANE SEGMENTS M1-M3 AND M4, AND THE CONNECTING LINKS M1-M2 AND M2-M3. THE EXTENDED LOOP BETWEEN M3 AND M4, FORMING THE INTRACELLULAR DOMAIN OF THE RECEPTOR, AND SEVERAL OF THE C -TERMINAL RESIDUES ON M4 (CHAINS B, C AND E) ARE OMITTED. THE LINK BETWEEN M1 AND M2 WAS POORLY RESOLVED AND THE TRACE HERE IS ALMOST CERTAINLY WRONG IN DETAIL. IT IS HOPED THAT WITH IMPROVED DATA AND WITH REFINEMENT A MORE ACCURATE MODEL WILL BE OBTAINED. THESE COORDINATES, INCLUDING ESTIMATES OF SIDE CHAIN POSITIONS, ARE BEING MADE AVAILABLE IN THE HOPE THAT THEY WILL BE USEFUL. USERS SHOULD BEAR IN MIND THAT BECAUSE OF THE LIMITED RESOLUTION THE CONFORMATIONS OF THE SIDE CHAINS AND THEIR ATOMIC COORDINATES ARE NOT INDIVIDUALLY RELIABLE. ALSO THE ENDS OF THE HELICES ARE UNCERTAIN BY AT LEAST ONE RESIDUE. THE SURFACE LATTICE OF THE TUBULAR CRYSTALS HAS P2 SYMMETRY. THE FOUR HELICAL FAMILIES, DEFINED BY THE NUMBERS OF THE TWO PRINCIPAL HELICES REQUIRED TO FILL 360 DEGREES OF AZIMUTH, WERE: (-16,6),(-18,6),(-17,5),(-15,7). NEGATIVE INDICATES LEFT-HANDED. TO COMPARE AND COMBINE FOURIER TERMS FROM WITHIN A FAMILY IT WAS USUALLY NECESSARY TO REASSIGN LAYER-LINES TO MATCH THOSE CORRESPONDING TO A STANDARD HELICAL SELECTION RULE DEFINING A TYPICAL SET OF POSITIONS IN THE TRANSFORM. THE STANDARD SELECTION RULES WERE: L = 113N' + 314M (N = 2N') (-16,6) L = 25N' + 112M (N = 6N') (-18,6) L = 247N + 605M (-17,5) L = -91N + 662M (-15,7) WHERE L IS THE LAYER-LINE NUMBER, M IS AN INTEGER, N IS THE START NUMBER (I.E. NUMBER AROUND THE CIRCUMFERENCE) OF THE CONTRIBUTING HELIX, AND N=2N' INDICATES THAT THE START NUMBERS OCCUR IN MULTIPLES OF 2.
Refine
Ls d res high4.0 A
Refine hist
D res high4.0
Solvent atoms0
Total atoms4926
Ligand atoms0
Nucleic acid atoms0
Protein atoms4926
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