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- EMDB-69322: Cryo-EM structure of the de novo designed metalloprotease DP622 E... -

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Basic information

Entry
Database: EMDB / ID: EMD-69322
TitleCryo-EM structure of the de novo designed metalloprotease DP622 E96Q mutant
Map data
Sample
  • Cell: de novo designed metalloprotease DP622 E96Q mutant
    • Protein or peptide: DP622
    • Protein or peptide: Amyloid-beta protein 42
  • Ligand: ZINC ION
Keywordsde novo designed metalloprotease / DE NOVO PROTEIN
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Golgi-associated vesicle / PTB domain binding / astrocyte projection / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / dendrite development / regulation of multicellular organism growth / nuclear envelope lumen / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / Notch signaling pathway / main axon / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / swimming behavior / adult locomotory behavior / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / extracellular matrix organization / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / astrocyte activation / regulation of neuron apoptotic process / Mitochondrial protein degradation / positive regulation of glycolytic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / learning / response to interleukin-1 / cellular response to cAMP / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / locomotory behavior / positive regulation of interleukin-1 beta production / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / visual learning / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / synapse organization / positive regulation of interleukin-6 production / recycling endosome / positive regulation of JNK cascade / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of inflammatory response / calcium ion transport / positive regulation of tumor necrosis factor production / regulation of translation / regulation of gene expression / Platelet degranulation / heparin binding
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsQu YN / Cao LX
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Vita / Year: 2026
Title: De novo design of metalloproteases for targeted amyloid-beta cleavage
Authors: Qu Y / Wang C / Zhu H / Wang Y / Cao L
History
DepositionFeb 23, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69322.png

Downloads & links

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Map

FileDownload / File: emd_69322.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 432 pix.
= 246.24 Å		0.57 Å/pix.
x 432 pix.
= 246.24 Å		0.57 Å/pix.
x 432 pix.
= 246.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.047
Minimum - Maximum-0.47220057 - 0.605101
Average (Standard dev.)-0.000058363523 (±0.005399468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 246.23999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_69322_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69322_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : de novo designed metalloprotease DP622 E96Q mutant

EntireName: de novo designed metalloprotease DP622 E96Q mutant
Components
  • Cell: de novo designed metalloprotease DP622 E96Q mutant
    • Protein or peptide: DP622
    • Protein or peptide: Amyloid-beta protein 42
  • Ligand: ZINC ION

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Supramolecule #1: de novo designed metalloprotease DP622 E96Q mutant

SupramoleculeName: de novo designed metalloprotease DP622 E96Q mutant / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DP622

MacromoleculeName: DP622 / type: protein_or_peptide / ID: 1 / Details: DP622 E96Q mutant / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 171.326141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH SSGLEVLFQG PGGTRNLELA RAADVTVTVA DTPEEMYEAA KVAVETVREL AAGDPRRDEY VALAERLFRT GIERGGIAG IAIYADGRRR VFVVAPSDAS DEALIYALAH QLAHLIIAED LERRGLPLSA VPPGVVEGLA DVFGATAYAA Y LELKGEKV ...String:
MGHHHHHHHH SSGLEVLFQG PGGTRNLELA RAADVTVTVA DTPEEMYEAA KVAVETVREL AAGDPRRDEY VALAERLFRT GIERGGIAG IAIYADGRRR VFVVAPSDAS DEALIYALAH QLAHLIIAED LERRGLPLSA VPPGVVEGLA DVFGATAYAA Y LELKGEKV TLEKWREMQL RLAEETERIG REAGLEAHVE GGRIAAEIAR RTNEEEAQKL IEEVKPLVEF ILGLLRVART AH RAVPGGR ATVTLKPDGL AEVELKGADP KNPAIAIIKV AAMLQGLLLR FPEDEEVHKL VVENLRILIE NLEKLVEKAE KDL NTNPEF IRQLAAALEL VAEVLRTILR FGKEELKEEA KELGRLLGEV ALKLLELLKK LLEKAEKEGN KEIHELIAEA IAAL IGVAD ALRRLGLEEE AEELKKKIAE LVNKLVESYP EQLFKLIEKT LDHPETLAEV LSQVKLTKEL AKELFEKALE AIKEK NYKL AYLYLTAAAT NPEMLPKIKE LLEKEEDIEV IKVIAKAAIT AANNENLTKE QAELLAELLL LALEKLIPDE ELLELI IKI LKALAKLFKK LDPKTAIEYL KKVTELVLEL LEREKDPERI IKLGEALAKL LEGVGENAAK TKDKELVKTA IELAKEV IE KILKRLLEDK SLSPEEVAAL VEAIVKIAEG TIKALILAGL LEEALEFLKE VLEKIVETIE QLPDELRPEA IAALLESL G ESLVEIAKTA LENLPEEEAE KFLKEVLRLI LEFLEKLFEI ALPLADDKEA VEKIMKGLAK LVGGLLVVLL LVPGVEEEV RRIIRLITEF IEEVFRRMVE KAETEEEREE VREFIAELLL EFLKIIGEKV VKGTEEAVRK GLLKPEGLRA ALRLLGELVE ALLRLAAEL LPEELAREVA REMLEIAFET LAEVLKVVSP DPLAAVEAAE AAFEVLLRLI RVAVELHGLD EEELVELAVR K LREARREI EKESREEREL ERRLLEIRAE IDPEEVAKEL EKEIEELKKN IEEALKKLEE FFEKVQERIK ELPERERELV EK LATAFLE LMLTVIRNSV ERLLELALLL AKVLVKLGKY EEAFEVIKEA VRLAKEVVRK LEELAERSES EELREHALET AAE ILARAI KALAEAIKAF ADKDPEIAEE LFELMLELLE ELERLVRRAV ERGFPRVVRH LGPAVKALAE AALHHPNREE ALER AVERL RRLLEELERL AERVEREEED PVRRLALLAA LAEAQVAVLE ALARLSEHLP EERRKEVEEW LKKRVLELLE RLLEL LREA EELYRRTGDE RLREIARELR RILERLAEVT EGSLELAEAA WELLAPHPEA FGARAEVVVN LAKLDPERGL RALEEL EKQ VSTEEQREAL AYALGRIVGY VDEERAKELI DRAIELGQYD AFAEGLAEAL LEAPEERIPK LLKAIEEFLK KLEEELK EI EKKINEPEFQ KSKDEEELEK IKKKIESIKR AAEKILKAAL KKILEEPELA LKVAELALKV IAKANKILEK L

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Macromolecule #2: Amyloid-beta protein 42

MacromoleculeName: Amyloid-beta protein 42 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.520087 KDa
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

UniProtKB: Amyloid-beta precursor protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 148591
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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