+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33189 | |||||||||
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Title | cryo-EM structure of hemoglobin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | tetramer / OXYGEN TRANSPORT | |||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Liu N / Wang HW | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Methods / Year: 2023 Title: Uniform thin ice on ultraflat graphene for high-resolution cryo-EM. Authors: Liming Zheng / Nan Liu / Xiaoyin Gao / Wenqing Zhu / Kun Liu / Cang Wu / Rui Yan / Jincan Zhang / Xin Gao / Yating Yao / Bing Deng / Jie Xu / Ye Lu / Zhongmin Liu / Mengsen Li / Xiaoding Wei ...Authors: Liming Zheng / Nan Liu / Xiaoyin Gao / Wenqing Zhu / Kun Liu / Cang Wu / Rui Yan / Jincan Zhang / Xin Gao / Yating Yao / Bing Deng / Jie Xu / Ye Lu / Zhongmin Liu / Mengsen Li / Xiaoding Wei / Hong-Wei Wang / Hailin Peng / Abstract: Cryo-electron microscopy (cryo-EM) visualizes the atomic structure of macromolecules that are embedded in vitrified thin ice at their close-to-native state. However, the homogeneity of ice thickness, ...Cryo-electron microscopy (cryo-EM) visualizes the atomic structure of macromolecules that are embedded in vitrified thin ice at their close-to-native state. However, the homogeneity of ice thickness, a key factor to ensure high image quality, is poorly controlled during specimen preparation and has become one of the main challenges for high-resolution cryo-EM. Here we found that the uniformity of thin ice relies on the surface flatness of the supporting film, and developed a method to use ultraflat graphene (UFG) as the support for cryo-EM specimen preparation to achieve better control of vitreous ice thickness. We show that the uniform thin ice on UFG improves the image quality of vitrified specimens. Using such a method we successfully determined the three-dimensional structures of hemoglobin (64 kDa), α-fetoprotein (67 kDa) with no symmetry, and streptavidin (52 kDa) at a resolution of 3.5 Å, 2.6 Å and 2.2 Å, respectively. Furthermore, our results demonstrate the potential of UFG for the fields of cryo-electron tomography and structure-based drug discovery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33189.map.gz | 6.4 MB | EMDB map data format | |
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Header (meta data) | emd-33189-v30.xml emd-33189.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_33189.png | 64.9 KB | ||
Masks | emd_33189_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-33189.cif.gz | 5.2 KB | ||
Others | emd_33189_half_map_1.map.gz emd_33189_half_map_2.map.gz | 48.5 MB 48.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33189 | HTTPS FTP |
-Validation report
Summary document | emd_33189_validation.pdf.gz | 736.5 KB | Display | EMDB validaton report |
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Full document | emd_33189_full_validation.pdf.gz | 736.1 KB | Display | |
Data in XML | emd_33189_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_33189_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33189 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33189 | HTTPS FTP |
-Related structure data
Related structure data | 7xgyMC 7yimC 8gvkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33189.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.5191 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33189_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33189_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33189_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hemoglobin
Entire | Name: hemoglobin |
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Components |
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-Supramolecule #1: hemoglobin
Supramolecule | Name: hemoglobin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Hemoglobin subunit alpha
Macromolecule | Name: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.28155 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHA HKLRVDPVNF KLLSHCLLVT LAAHLPAEFT PAVHASLDKF LASVSTVLTS KYR UniProtKB: Hemoglobin subunit alpha |
-Macromolecule #2: Hemoglobin subunit beta
Macromolecule | Name: Hemoglobin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.021396 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATL SELHCDKLHV DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA NALAHKYH UniProtKB: Hemoglobin subunit beta |
-Macromolecule #3: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 3 / Number of copies: 4 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105000 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |