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Open data
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Basic information
Entry | Database: PDB / ID: 9vid | ||||||
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Title | cryo-EM structure of alligator haemoglobin in the R conformation | ||||||
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![]() | OXYGEN BINDING / haemoglobin | ||||||
Function / homology | ![]() haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å | ||||||
![]() | Takahashi, K. / Lee, Y. / Nishizawa, T. / Tame, J.R.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational analysis of liganded human hemoglobin by cryo electron microscopy Authors: Takahashi, K. / Lee, Y. / Nishizawa, T. / Tame, J.R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 51.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 65084MC ![]() 9vibC ![]() 9vicC ![]() 9vieC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 15891.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P01999 | ||||||
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#2: Protein | Mass: 16641.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P02130 | ||||||
#3: Chemical | #4: Chemical | Has ligand of interest | Y | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: alligator haemoglobin in carboxy form / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Value: 0.1 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371597 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8WIX Accession code: 8WIX / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.22→2.22 Å / Cor.coef. Fo:Fc: 0.849 / SU B: 3.455 / SU ML: 0.078 / ESU R: 0.127 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.332 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 2373 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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