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

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Basic information

Entry
Database: PDB / ID: 7vqo
TitleCryo-EM structure of Ams1 bound to the FW domain of Nbr1
ComponentsAms1, Nbr1 and malE fusion protein
KeywordsHYDROLASE / glycoside hydrolase / signaling protein / autophagy
Function / homology
Function and homology information


alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / phagophore assembly site / fungal-type vacuole membrane / oligosaccharide catabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity ...alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / phagophore assembly site / fungal-type vacuole membrane / oligosaccharide catabolic process / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / ubiquitin binding / cell chemotaxis / macroautophagy / outer membrane-bounded periplasmic space / carbohydrate binding / periplasmic space / DNA damage response / zinc ion binding / metal ion binding / membrane
Similarity search - Function
: / Alpha-mannosidase, jelly roll 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 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase family 38, N-terminal domain ...: / Alpha-mannosidase, jelly roll 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 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 / 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 families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal 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. / Beta-galactosidase; Chain A, domain 5 / 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 / Distorted Sandwich / Alpha-Beta Barrel / Immunoglobulin-like fold / Mainly Beta / Alpha Beta
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)
Chaetomium thermophilum DSM 1495 (fungus)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsZhang, J. / Ye, K.
Funding support China, 3items
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, Y.Y. / Pan, Z.Q. / Li, Y. / Sui, J. / Du, L.L. / Ye, K.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ams1, Nbr1 and malE fusion protein
B: Ams1, Nbr1 and malE fusion protein
C: Ams1, Nbr1 and malE fusion protein
D: Ams1, Nbr1 and malE fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)726,9678
Polymers726,7054
Non-polymers2624
Water12,394688
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "D"
d_4ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYALAALACC2 - 10792 - 1079
d_12LEULEULYSLYSCC1122 - 12451122 - 1245
d_21GLYGLYALAALABB2 - 10792 - 1079
d_22LEULEULYSLYSBB1122 - 12451122 - 1245
d_31GLYGLYALAALADD2 - 10792 - 1079
d_32LEULEULYSLYSDD1122 - 12451122 - 1245
d_41GLYGLYALAALAAA2 - 10792 - 1079
d_42LEULEULYSLYSAA1122 - 12451122 - 1245

NCS oper:
IDCodeMatrixVector
1given(-0.999999999802, -1.3943597465E-5, -1.41711530355E-5), (-1.39413008959E-5, 0.999999986773, -0.000162046617959), (1.41734123609E-5, -0.000162046420363, -0.99999998677)166.403630754, 0.0117457769982, 135.210096671
2given(0.999999999739, 1.63022703359E-5, 1.59913533248E-5), (1.62996573275E-5, -0.999999986519, 0.000163387853961), (1.59940167022E-5, -0.000163387593265, -0.999999986524)-0.00402547952744, 141.42792085, 135.21006773
3given(-0.99999997551, 9.50705145044E-5, -0.000199852652478), (-9.51149472286E-5, -0.999999970761, 0.000222329671678), (-0.000199831509638, 0.000222348675207, 0.999999955314)166.415226073, 141.438896393, -0.00175645367725

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Components

#1: Protein
Ams1, Nbr1 and malE fusion protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 181676.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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).
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus), (gene. exp.) Chaetomium thermophilum DSM 1495 (fungus), (gene. exp.) Escherichia coli K-12 (bacteria)
Strain: DSM 1495, K-12 / Gene: CTHT_0067100, CTHT_0062850, malE / Production host: Schizosaccharomyces pombe 972h- (yeast)
References: UniProt: G0SGP6, UniProt: G0SE85, UniProt: P0AEX9, alpha-mannosidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ams1, Nbr1 and malE fusion protein / Type: COMPLEX
Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP).
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.52 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)759272DSM 1495
21Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)759272DSM 1495
31Escherichia coli K-12 (bacteria)83333K-12
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Schizosaccharomyces pombe 972h- (yeast)284812
21Schizosaccharomyces pombe 972h- (yeast)284812
31Schizosaccharomyces pombe 972h- (yeast)284812
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris hydrochlorideTris-HCl1
2150 mMSodium chlorideNaCl1
35 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: NICKEL/TITANIUM / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2925
EM imaging opticsEnergyfilter name: GIF Tridiem 4K / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 32

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
7Cootmodel fitting
9cryoSPARC2.5initial Euler assignment
10cryoSPARC2.5final Euler assignment
11cryoSPARC2.5classification
12cryoSPARC2.53D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 692409 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6LZ1

6lz1


Accession code: 6LZ1 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008539012
ELECTRON MICROSCOPYf_angle_d0.793252992
ELECTRON MICROSCOPYf_chiral_restr0.05075620
ELECTRON MICROSCOPYf_plane_restr0.00436860
ELECTRON MICROSCOPYf_dihedral_angle_d30.64875140
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDTypeRms dev position (Å)
ens_1d_2ELECTRON MICROSCOPYNCS constraints0.000705156596324
ens_1d_3ELECTRON MICROSCOPYNCS constraints0.000706146254275
ens_1d_4ELECTRON MICROSCOPYNCS constraints0.000705685865871

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