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- PDB-4v93: Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM co... -
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Basic information
Entry | Database: PDB / ID: 4v93 | |||||||||
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Title | Fitted coordinates for Lumbricus terrestris hemoglobin cryo-EM complex (EMD-2627) | |||||||||
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![]() | TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
![]() | Chen, W.T. / Chen, Y.C. / Liou, H.H. / Chao, C.Y. | |||||||||
![]() | ![]() 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. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 4.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 641.4 KB | Display | |
Data in CIF | ![]() | 1012.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2627MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-EXTRACELLULAR GLOBIN- ... , 5 types, 108 molecules A0A5ACAHAMARAWAbAgAlAqAvA2A3A7AAAEAFAJAKAOAPATAUAYAZAdAeAiAj...
#1: Protein | Mass: 16902.410 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 17136.619 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 16268.229 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 17566.990 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 19126.137 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-HEMOGLOBIN CHAIN ... , 2 types, 36 molecules A1A6ADAIANASAXAcAhAmArAwB0B5BCBHBMBRBWBbBgBlBqBvC4CBCGCLCQCV...
#2: Protein | Mass: 15988.263 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 17948.670 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 1 types, 12 molecules C0C5CCCHCMCRCWCbCgClCqCv
#8: Protein | Mass: 27460.688 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-EXTRACELLULAR HEMOGLOBIN LINKER ... , 2 types, 24 molecules C1C6CDCICNCSCXCcChCmCrCwC2C7CECJCOCTCYCdCiCnCsCx
#9: Protein | Mass: 32075.490 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 26877.914 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-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: Lumbricus terrestris hemoglobin / Type: COMPLEX |
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Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 15, 2012 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 80000 X |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||
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3D reconstruction | Resolution: 8.1 Å / Num. of particles: 4500 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2627. (DEPOSITION ID: 12397). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Details: REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 2GTL | ||||||||||||
Refinement | Highest resolution: 8.1 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.1 Å
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