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Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.

by single particle reconstruction, at 9.1 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0055, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0055, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1434
TitleNautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
MapThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
SampleNautilus pompilius hemocyanin
AuthorsGatsogiannis C, Moeller A, Depoix F, Meissner U, Markl J
DateDeposition: 2007-09-26, Header release: 2007-09-26, Map release: 2011-09-30, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0055, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0055, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 374, Issue 2, Page 465-86, Year 2007
TitleNautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
AuthorsChristos Gatsogiannis, Arne Moeller, Frank Depoix, Ulrich Meissner, Jürgen Markl
Institute of Zoology, Johannes Gutenberg University, D-55099 Mainz, Germany.
KeywordsAmino Acid Sequence, Animals, Binding Sites, Cryoelectron Microscopy, Hemocyanin (ultrastructure, 9013-72-3), Image Processing, Computer-Assisted, Models, Molecular, Molecular Sequence Data, Nautilus (chemistry), Octopodiformes (chemistry), Protein Conformation, Sequence Homology, Amino Acid
LinksPII: S0022-2836(07)01224-7, DOI: 10.1016/j.jmb.2007.09.036, PubMed: 17936782
Map
Fileemd_1434.map.gz ( map file in CCP4 format, 65537 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.85 A/pix
= 473.6 A
256 pix
1.85 A/pix
= 473.6 A
256 pix
1.85 A/pix
= 473.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0055 (by emdb), 0.0055 (movie #1):
Minimum - Maximum: -0.0368309 - 0.0538236
Average (Standard dev.): 0.000232174 (0.00402936)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
Unit CellA= B= C: 473.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.85 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.851.851.85
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z473.600473.600473.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ10110173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0370.0540.000
Annotation DetailsThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
Supplement
Images
Images
Sample
NameNautilus pompilius hemocyanin
Oligomeric StateNautilus pompilius hemocyanin is a decamer of a 350 kDa subunit. Each subunit is composed by 7 paralogous O2 binding functional units.
Number of Components1
Theoretical Mass3.5MDa
Component #1: protein - Nautilus pompilius hemocyanin
Scientific nameNautilus pompilius hemocyanin
Experimental Mass3.5 MDa
Scientific Name of SpeciesNautilus pompilius
NCBI taxonomy34573
Recombinant expressionNo
Natural SourceOrgan Or Tissue: hemolymph
Experiment
Sample Preparation
Specimen Conc0.4 mg/ml
Stainingcryo-EM, no stain
Specimen Support Details400 mesh copper
Specimen Stateparticle
BufferDetails: 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, 150mM NaCl
pH: 7.4
Vitrification
MethodSingle side blotting and rapid plunging
Cryogen NameETHANE
DetailsVitrification instrument: home made. Vitrification carried out in 100 percent nitrogen atmosphere
InstrumentHOMEMADE PLUNGER
Temperature86 Kelvin
Imaging
MicroscopeFEI TECNAI F30
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeOTHER
Lens
MagnificationNominal: 49000, Calibrated: 49000
Nominal Cs1.2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 3300 nm
Specimen Holder
HolderGatan single-tilt cryoholder
ModelGATAN LIQUID NITROGEN
Temperature86 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images63
Sampling Size1.86
Quant Bit Number8
ScannerPRIMESCAN
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCommon Lines, projection matching
SoftwareIMAGIC-5
CTF CorrectionCTFFIND3 and TRANSFER, IMAGIC 5
Resolution By Author9.1 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages5200
Number of Projections16000
DetailsThe particles were selected using the automatic selection program boxer
Applied SymmetryC5 (5 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1434.xml (7.4 KB)
Map dataemd_1434.map.gz (60.1 MB)
Imagesem-1434.png (422 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1434
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.7 KB