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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | PaaZ, bifunctional enzyme | |||||||||
![]() | Relion sharpened full map | |||||||||
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![]() | Hydrolase / dehydrogenase / Bi-functional enzyme | |||||||||
Function / homology | ![]() 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase / oxepin-CoA hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / ether hydrolase activity / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / phenylacetate catabolic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / enoyl-CoA hydratase activity / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Yadav S / Vinothkumar KR | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Factors affecting macromolecule orientations in thin films formed in cryo-EM. Authors: Swati Yadav / Kutti R Vinothkumar / ![]() Abstract: The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the ...The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9 KB | Display | ![]() |
Images | ![]() | 39.9 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 49.5 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 990.9 KB | Display | ![]() |
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Full document | ![]() | 990.5 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wv6MC ![]() 8wv4C ![]() 8wv5C ![]() 8wzhC ![]() 8wziC ![]() 8wzjC ![]() 8wzkC ![]() 8wzmC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Relion sharpened full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Relion sharpened half map
File | emd_37866_half_map_1.map | ||||||||||||
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Annotation | Relion sharpened half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion sharpened half map
File | emd_37866_half_map_2.map | ||||||||||||
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Annotation | Relion sharpened half map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : PaaZ, bifunctional enzyme
Entire | Name: PaaZ, bifunctional enzyme |
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Components |
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-Supramolecule #1: PaaZ, bifunctional enzyme
Supramolecule | Name: PaaZ, bifunctional enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 438 KDa |
-Macromolecule #1: Bifunctional protein PaaZ
Macromolecule | Name: Bifunctional protein PaaZ / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 73.969391 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGHHHHHHQQ LASFLSGTWQ SGRGRSRLIH HAISGEALWE VTSEGLDMAA ARQFAIEKGA PALRAMTFIE RAAMLKAVAK HLLSEKERF YALSAQTGAT RADSWVDIEG GIGTLFTYAS LGSRELPDDT LWPEDELIPL SKEGGFAARH LLTSKSGVAV H INAFNFPC ...String: MGHHHHHHQQ LASFLSGTWQ SGRGRSRLIH HAISGEALWE VTSEGLDMAA ARQFAIEKGA PALRAMTFIE RAAMLKAVAK HLLSEKERF YALSAQTGAT RADSWVDIEG GIGTLFTYAS LGSRELPDDT LWPEDELIPL SKEGGFAARH LLTSKSGVAV H INAFNFPC WGMLEKLAPT WLGGMPAIIK PATATAQLTQ AMVKSIVDSG LVPEGAISLI CGSAGDLLDH LDSQDVVTFT GS AATGQML RVQPNIVAKS IPFTMEADSL NCCVLGEDVT PDQPEFALFI REVVREMTTK AGQKCTAIRR IIVPQALVNA VSD ALVARL QKVVVGDPAQ EGVKMGALVN AEQRADVQEK VNILLAAGCE IRLGGQADLS AAGAFFPPTL LYCPQPDETP AVHA TEAFG PVATLMPAQN QRHALQLACA GGGSLAGTLV TADPQIARQF IADAARTHGR IQILNEESAK ESTGHGSPLP QLVHG GPGR AGGGEELGGL RAVKHYMQRT AVQGSPTMLA AISKQWVRGA KVEEDRIHPF RKYFEELQPG DSLLTPRRTM TEADIV NFA CLSGDHFYAH MDKIAAAESI FGERVVHGYF VLSAAAGLFV DAGVGPVIAN YGLESLRFIE PVKPGDTIQV RLTCKRK TL KKQRSAEEKP TGVVEWAVEV FNQHQTPVAL YSILTLVARQ HGDFVD UniProtKB: Bifunctional protein PaaZ |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 288 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.8 mg/mL | ||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force, 0. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 60.0 sec. / Average electron dose: 25.0 e/Å2 Details: Images were collected in movie mode at 40 frames per second. Total of 25 frames were saved |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |