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- EMDB-32091: Cryo-EM structure of Ams1 bound to the FW domain of Nbr1 -

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Basic information

Entry
Database: EMDB / ID: EMD-32091
TitleCryo-EM structure of Ams1 bound to the FW domain of Nbr1
Map data
Sample
  • Complex: Ams1, Nbr1 and malE fusion protein
    • Protein or peptide: Ams1, Nbr1 and malE fusion protein
  • Ligand: ZINC ION
  • Ligand: water
Function / homology
Function and homology information


alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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
Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain ...Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Galactose mutarotase-like domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin-like fold
Similarity search - Domain/homology
Zinc-binding domain-containing protein / Alpha-mannosidase / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsZhang J / Ye K
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071199, 91940302 China
Chinese Academy of SciencesXDB37010201 China
National Basic Research Program of China (973 Program)2017YFA0504600 China
CitationJournal: 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
DepositionOct 20, 2021-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32091.png

Downloads & links

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Map

FileDownload / File: emd_32091.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-38.770523 - 70.62753
Average (Standard dev.)0.052148692 (±2.4435465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32091_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32091_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ams1, Nbr1 and malE fusion protein

EntireName: Ams1, Nbr1 and malE fusion protein
Components
  • Complex: Ams1, Nbr1 and malE fusion protein
    • Protein or peptide: Ams1, Nbr1 and malE fusion protein
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Ams1, Nbr1 and malE fusion protein

SupramoleculeName: 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).
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495
Recombinant expressionOrganism: Schizosaccharomyces pombe 972h- (yeast)
Molecular weightTheoretical: 520 KDa

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Macromolecule #1: Ams1, Nbr1 and malE fusion protein

MacromoleculeName: 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
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 181.67625 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe 972h- (yeast)
SequenceString: 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 688 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HClTrisTris hydrochloride
150.0 mMNaClSodium chlorideSodium chloride
5.0 mMMgCl2Magnesium chloride
GridModel: Homemade / Material: NICKEL/TITANIUM / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Name: GIF Tridiem 4K / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2925 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

30021

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 692409
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6lz1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Output model

PDB-7vqo:
Cryo-EM structure of Ams1 bound to the FW domain of Nbr1

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