+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32091 | ||||||||||||
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Title | Cryo-EM structure of Ams1 bound to the FW domain of Nbr1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | glycoside hydrolase / signaling protein / HYDROLASE / autophagy | ||||||||||||
Function / homology | Function and homology information alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / periplasmic space / DNA damage response / zinc ion binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Escherichia coli K-12 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.19 Å | ||||||||||||
Authors | Zhang J / Ye K | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1 Authors: Zhang J / Wang YY / Pan ZQ / Li Y / Sui J / Du LL / Ye K | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32091.map.gz | 4.5 MB | EMDB map data format | |
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Header (meta data) | emd-32091-v30.xml emd-32091.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32091_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_32091.png | 179.4 KB | ||
Masks | emd_32091_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-32091.cif.gz | 7.3 KB | ||
Others | emd_32091_half_map_1.map.gz emd_32091_half_map_2.map.gz | 115.1 MB 115.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32091 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32091 | HTTPS FTP |
-Validation report
Summary document | emd_32091_validation.pdf.gz | 722.1 KB | Display | EMDB validaton report |
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Full document | emd_32091_full_validation.pdf.gz | 721.7 KB | Display | |
Data in XML | emd_32091_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_32091_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32091 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32091 | HTTPS FTP |
-Related structure data
Related structure data | 7vqoMC 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_32091.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_32091_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32091_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32091_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ams1, Nbr1 and malE fusion protein
Entire | Name: Ams1, Nbr1 and malE fusion protein |
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Components |
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-Supramolecule #1: Ams1, Nbr1 and malE fusion protein
Supramolecule | Name: Ams1, Nbr1 and malE fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP). |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 |
Molecular weight | Theoretical: 520 KDa |
-Macromolecule #1: Ams1, Nbr1 and malE fusion protein
Macromolecule | Name: Ams1, Nbr1 and malE fusion protein / type: protein_or_peptide / ID: 1 Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP).,The fusion protein ...Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP).,The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP). Number of copies: 4 / Enantiomer: LEVO / EC number: alpha-mannosidase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Molecular weight | Theoretical: 181.67625 KDa |
Recombinant expression | Organism: Schizosaccharomyces pombe 972h- (yeast) |
Sequence | String: MGGETFDVKG PRPNDYPLRA PKPVGQLISH IYKDRIAQFY NGGQYEHQNL RAMMKEDSVS GEPHVQLWVW HAPGQTRPSF EEAVSNQFV KTNVGEWFGP SWTTHWFRVV LTVPEHLQNK RLLEFHWDSN SEGLVWSEDG KPLQGLTGGG ERVEWILPDS F RDGKEHTI ...String: MGGETFDVKG PRPNDYPLRA PKPVGQLISH IYKDRIAQFY NGGQYEHQNL RAMMKEDSVS GEPHVQLWVW HAPGQTRPSF EEAVSNQFV KTNVGEWFGP SWTTHWFRVV LTVPEHLQNK RLLEFHWDSN SEGLVWSEDG KPLQGLTGGG ERVEWILPDS F RDGKEHTI YIEMACNRMF GNAPGGDSIQ PPDPNKYFRL DKAEIVAIDP DARQLWIDIW ILQDAAREFP GDSWESHKAL QV CNEIIEA FELGNRESLK KCRKIAEQYL GPNVDSPNVY NSGKEPLVYA IGHCHIDSCW LWPFAETKRK VVRSWSSQCD LMD RYPELN FVCSQAQQYK WLKQLYPYAF ERVKKKVAEG RFHPIGGSWV EHDTNMPSGE SLVRQFLYGQ RFYESNFGKR CKTF WLPDT FGYSAQLPQL CRLAGMTRFL TQKLSWNNIN RFPHTTFNWV ALDGSQVICH MPPSETYTAE AHFGDVKRSM SQHKS LDQD NTSLLVFGKG DGGGGPTWVQ IEKLRRCRGI SDTVGLLPRV HMGSSVDDFF DRLERKADTF VTWYGELYFE LHRGTY TTQ AKNKKNNRRA EAKLRDLELL ATIASVQDKS YKYPKEEFDA MWENVLLCQF HDCLPGSSIE MAYRESDQMY ADVFSTA EK IMKGVSQVLG LEPALNHMST TNTVALNTLP WPRRELVKIS EKEAAVAHGT GPFLKLQKLE TTKPLVTLRQ VTKGAFVL E NSQLRVHVEK GVITSLYDKQ ANREVIPKGQ KANQYVIFDD KPLYWQAWDV EVYHLDTRKE LPSGETEVHE NTPHRVSVV TRTKVSDKSH IQTIIALNGA VEGEQSWVEV QSKVDWHETM KFLKVEFPVD VRNTEASYET AFGIVRRPTH YNTSWDMAKF EVCAHRWAD LSEYGYGVSI LNDSKYGFAT AGQTMRLSLL RSPKAPDAHA DMGTHHIRWA ILPHQGSLSH VTIRKAFEFN N PTKLYSSP DAAALVAAPP PVWLTPDSSP AIVLDTVKRG EDDEDVSRGE LPARKGQSVI LRMYDSLGGL ARGTVVTTWP LK KVCKVNL LEDDLEVVPW ENGRFTVELR PFEVASYRLV LAGGGGSGGG FKKASSSDNK EQGGGGSGGG SGEPVVEKEP SAE ELEATF VRDTVQDGTV LAPNHLFEQT WVLRNTGKVA WPAGCSVKFV GGDYMGRVDS AHPAASKEVE ESCESTVCDR AVQP GEEAP FTVLLRTPYR ACRVISHWRL TTPKGTKFGH RLWCDVVVEK PKSRSKIEEG KLVIWINGDK GYNGLAEVGK KFEKD TGIK VTVEHPDKLE EKFPQVAATG DGPDIIFWAH DRFGGYAQSG LLAEITPDKA FQDKLYPFTW DAVRYNGKLI AYPIAV EAL SLIYNKDLLP NPPKTWEEIP ALDKELKAKG KSALMFNLQE PYFTWPLIAA DGGYAFKYEN GKYDIKDVGV DNAGAKA GL TFLVDLIKNK HMNADTDYSI AEAAFNKGET AMTINGPWAW SNIDTSKVNY GVTVLPTFKG QPSKPFVGVL SAGINAAS P NKELAKEFLE NYLLTDEGLE AVNKDKPLGA VALKSYEEEL AKDPRIAATM ENAQKGEIMP NIPQMSAFWY AVRTAVINA ASGRQTVDEA LKDAQT UniProtKB: alpha-mannosidase, Zinc-binding domain-containing protein, Maltose/maltodextrin-binding periplasmic protein |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 688 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Homemade / Material: NICKEL/TITANIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Tridiem 4K / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2925 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |