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- EMDB-2627: Electron cryo-microscopy of Lumbricus terrestris hemoglobin -

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Basic information

Entry
Database: EMDB / ID: EMD-2627
TitleElectron cryo-microscopy of Lumbricus terrestris hemoglobin
Map datasingle particle reconstruction of Lumbricus terrestris hemoglobin in oxygenated state
Sample
  • Sample: Lumbricus terrestris hemoglobin
  • Protein or peptide: Lumbricus terrestris hemoglobin
KeywordsLumbricus terrestris / hemoglobin
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. ...Annelid erythrocruorin linker subunit, C-terminal / Erythrocruorin linker subunit, C-terminal superfamily / Extracellular hemoglobin linker subunit, heterodimerisation domain / Annelid erythrocruorin linker subunit C-terminus / Globin, extracellular / Erythrocruorin / Low-density lipoprotein receptor domain class A / Myoglobin-like, M family globin domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Extracellular globin / Extracellular globin-2 / Extracellular globin-3 / Extracellular globin-4 / Extracellular hemoglobin linker L3 subunit / Extracellular hemoglobin linker L2 subunit / Hemoglobin linker chain L1
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsChen WT / Chen YC / Liou HH / Chao CY
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin.
Authors: Wei-Ting Chen / Yu-Chuen Chen / Horng-Huei Liou / Chih-Yu Chao /
Abstract: The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to ...The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure.
History
DepositionApr 9, 2014-
Header (metadata) releaseApr 23, 2014-
Map releaseApr 23, 2014-
UpdateMay 6, 2015-
Current statusMay 6, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v93
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2627.tif

Downloads & links

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Map

FileDownload / File: emd_2627.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsingle particle reconstruction of Lumbricus terrestris hemoglobin in oxygenated state
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.12996706 - 0.14308108
Average (Standard dev.)-0.00005797 (±0.01367736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 520.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.1300.143-0.000

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Supplemental data

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Sample components

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Entire : Lumbricus terrestris hemoglobin

EntireName: Lumbricus terrestris hemoglobin
Components
  • Sample: Lumbricus terrestris hemoglobin
  • Protein or peptide: Lumbricus terrestris hemoglobin

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Supramolecule #1000: Lumbricus terrestris hemoglobin

SupramoleculeName: Lumbricus terrestris hemoglobin / type: sample / ID: 1000 / Oligomeric state: 12 mer / Number unique components: 1
Molecular weightTheoretical: 3.6 MDa

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Macromolecule #1: Lumbricus terrestris hemoglobin

MacromoleculeName: Lumbricus terrestris hemoglobin / type: protein_or_peptide / ID: 1 / Oligomeric state: 12 mer / Recombinant expression: No
Source (natural)Organism: Lumbricus terrestris (common earthworm) / synonym: common earthworm
Molecular weightTheoretical: 3.6 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2 / Details: 50 mM Tris-HCl, 10 mM CaCl2, 10 mM MgCl2
GridDetails: Holy carbon on top of 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 15, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 250
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 80000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: micrograph
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC / Number images used: 4500

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Atomic model buiding 1

Initial modelPDB ID:

2gtl

SoftwareName: Chimera, Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-4v93:
Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex (EMD-2627)

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