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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, Made by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1434
AuthorsGatsogiannis C, Moeller A, Depoix F, Meissner U, Markl J
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

Supplemental images

em-1434.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

EMDB-5223

EMDB-1106
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 ( map file in CCP4 format, 67109 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.0055 (by emdb), 0.0055 (movie #1):
Minimum - Maximum: -0.0368309 - 0.0538236
Average (Standard dev.): 0.000232174 (0.00402936)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 256 256 256
Origin : 0 0 0
Limit : 255 255 255
Spacing : 256 256 256
Unit CellA = 473.6 A , B = 473.6 A , C = 473.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.85 A , Y = 1.85 A , 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

em-1434.png
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 Mass3.5 MDa
Component #1: protein - Nautilus pompilius hemocyanin
Scientific nameNautilus pompilius hemocyanin
Experimental Mass3.5 MDa
Scientific Name of SpeciesNautilus pompilius (NCBI Taxonomy: 34573)
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 X, Calibrated: 49000 X
Nominal Cs1.2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 3300 nm
Specimen Holder
HolderGatan single-tilt cryoholder ( GATAN LIQUID NITROGEN )
Temperature86 Kelvin
Camera
DetectorKodak SO163
Image Acquisition
Number of Digital Images63
Sampling Size1.86 microns
Quant Bit Number8
ScannerPRIMESCAN
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmCommon Lines, projection matching
SoftwareIMAGIC-5
CTF CorrectionCTFFIND3 and TRANSFER, IMAGIC 5
Resolution By Author9.1
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages5200
Number of Projections16000
DetailsThe particles were selected using the automatic selection program boxer
Download
Data from EMDB
Header (meta data in XML format)emd-1434.xml (7.3 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