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- EMDB-73489: Computationally Designed Tetramer of Apo-HC4 (C1 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-73489
TitleComputationally Designed Tetramer of Apo-HC4 (C1 symmetry)
Map dataComputationally Designed Tetramer of Apo-HC4 (C1 symmetry)
Sample
  • Complex: Tetrameric HC4 construct
    • Protein or peptide: Designed tetrameric HC4 protein.
KeywordsTetramer / computationally designed protein / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.34 Å
AuthorsEng VH / Narehood SM / Tezcan FA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-2038238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R24GM154186 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Computational Design of a Highly Stable Dicopper Catechol Oxidase
Authors: Eng VH / Narehood SM / Li Y / Gascon M / Hoffnagle AM / Shiau AA / Semonis M / Green MT / Britt RD / Tezcan FA
History
DepositionOct 21, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73489.png

Downloads & links

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Map

FileDownload / File: emd_73489.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComputationally Designed Tetramer of Apo-HC4 (C1 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 128 pix.
= 220.16 Å		1.72 Å/pix.
x 128 pix.
= 220.16 Å		1.72 Å/pix.
x 128 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.201
Minimum - Maximum-0.6824584 - 1.2254548
Average (Standard dev.)0.0008056739 (±0.030728243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_73489_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73489_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric HC4 construct

EntireName: Tetrameric HC4 construct
Components
  • Complex: Tetrameric HC4 construct
    • Protein or peptide: Designed tetrameric HC4 protein.

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Supramolecule #1: Tetrameric HC4 construct

SupramoleculeName: Tetrameric HC4 construct / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Designed tetrameric HC4 protein.

MacromoleculeName: Designed tetrameric HC4 protein. / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.233727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SKTDKLLELA KLELILNFFL LASNANITKE SFLIAHKAWH KALNKLYEID KELAKEYFYY MHSFSIPYYE KLGFKDVAEW HKVMVEYFK VGDKDEALEL HNEGHKALRA GDEEKFAALL KKARELIEKA KSAENLYFQ

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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

Concentration5 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Details: 9030 micrographs were collected with an untilted stage, and 6556 micrographs were collected at a 30 degree tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1246974
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 108599
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ytq:
Computationally Designed Tetramer of Apo-HC4 (C1 symmetry)

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