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- EMDB-72660: HCMV Protease in complex with Fab5 - Class 3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72660
TitleHCMV Protease in complex with Fab5 - Class 3
Map data
Sample
  • Complex: Complex of Fab5 and human cytomegalovirus protease
    • Complex: Fab5
      • Complex: Fab5 heavy chain
        • Protein or peptide: Fab5 Heavy Chain
      • Complex: Fab5 light chain
        • Protein or peptide: Fab5 light chain
    • Complex: Human cytomegalovirus protease
      • Protein or peptide: Assemblin
KeywordsCytomegalovirus / protease / antibody / complex / HYDROLASE
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21)
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesCytomegalovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZimanyi M / Hulce KR / Bohn MF / Norman J / Rohweder PJ / Detomasi TC / Cheng Y / Craik C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170792 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Antibody-Mediated Inhibition of Human Cytomegalovirus Protease Through a Conserved Cryptic Site
Authors: Zimanyi M / Hulce KR / Bohn MF / Norman J / Rohweder PJ / Cheng Y / Craik C
History
DepositionSep 10, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72660.png

Downloads & links

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Map

FileDownload / File: emd_72660.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 360 pix.
= 267.48 Å		0.74 Å/pix.
x 360 pix.
= 267.48 Å		0.74 Å/pix.
x 360 pix.
= 267.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.25250608 - 0.4811665
Average (Standard dev.)-0.00018181354 (±0.007167378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 267.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72660_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_72660_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 : Complex of Fab5 and human cytomegalovirus protease

EntireName: Complex of Fab5 and human cytomegalovirus protease
Components
  • Complex: Complex of Fab5 and human cytomegalovirus protease
    • Complex: Fab5
      • Complex: Fab5 heavy chain
        • Protein or peptide: Fab5 Heavy Chain
      • Complex: Fab5 light chain
        • Protein or peptide: Fab5 light chain
    • Complex: Human cytomegalovirus protease
      • Protein or peptide: Assemblin

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Supramolecule #1: Complex of Fab5 and human cytomegalovirus protease

SupramoleculeName: Complex of Fab5 and human cytomegalovirus protease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Fab fragment isolated from fully human naive phage-displayed library
Source (natural)Organism: Cytomegalovirus

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Supramolecule #2: Fab5

SupramoleculeName: Fab5 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human cytomegalovirus protease

SupramoleculeName: Human cytomegalovirus protease / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Cytomegalovirus

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Supramolecule #4: Fab5 heavy chain

SupramoleculeName: Fab5 heavy chain / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Fab5 light chain

SupramoleculeName: Fab5 light chain / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Assemblin

MacromoleculeName: Assemblin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: assemblin
Source (natural)Organism: Cytomegalovirus
Molecular weightTheoretical: 29.089678 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MHHHHHHMTM DEQQSQAVAP VYVGGFLARY DQSPDEAELL LPRDVVEHWL HAQGQGQPSL SVALPLNINH DDTAVVGHVA AMQSVRDGL FCLGCVTSPR FLEIVRRASE KSELVSRGPV SPLQPDKVVE FLSGSYAGLS LSSRRCDDVE VATSLSGSET T PFKHVALC ...String:
MHHHHHHMTM DEQQSQAVAP VYVGGFLARY DQSPDEAELL LPRDVVEHWL HAQGQGQPSL SVALPLNINH DDTAVVGHVA AMQSVRDGL FCLGCVTSPR FLEIVRRASE KSELVSRGPV SPLQPDKVVE FLSGSYAGLS LSSRRCDDVE VATSLSGSET T PFKHVALC SVGRRRGTLA VYGRDPEWVT QRFPDLTAAD RDGLRAQWQR CGSTAVDVSG DPFRSDSYGL LGNSVDALYI RE RLPKLRY DKQLVGVTER ESYVKA

UniProtKB: Capsid scaffolding protein

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Macromolecule #2: Fab5 Heavy Chain

MacromoleculeName: Fab5 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.942961 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: QVQLVQSGGG LVQPGRSLRL SCTASGFTFG DYAMSWFRQA PGKGLEWVGF IRSKAYGGTT EYAASVKGRF TISRDDSKSI AYLQMNSLK TEDTALYYCV VYNYYNYGMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGGG LVQPGRSLRL SCTASGFTFG DYAMSWFRQA PGKGLEWVGF IRSKAYGGTT EYAASVKGRF TISRDDSKSI AYLQMNSLK TEDTALYYCV VYNYYNYGMD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCAAAH HHHHH

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Macromolecule #3: Fab5 light chain

MacromoleculeName: Fab5 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.970748 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: LDVVMTQSPL SLPVTPGEPA SISCRSSQSL LHSNGYNYLD WYLQKPGQSP QLLIYLGSNR ASGVPDRFSG SGSGTDFTLK ISRVEAEDV GVYYCMQALQ TPITFGPGTK VDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
LDVVMTQSPL SLPVTPGEPA SISCRSSQSL LHSNGYNYLD WYLQKPGQSP QLLIYLGSNR ASGVPDRFSG SGSGTDFTLK ISRVEAEDV GVYYCMQALQ TPITFGPGTK VDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMKClpotassium chloride
25.0 mMK2HPO4potassium phosphate

Details: 25 mM potassium phosphate, 150 mM potassium chloride, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 6 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Number grids imaged: 1 / Number real images: 4538 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2820568
Details: All in cryoSPARC: Patch motion correction, patch CTF, micrograph denoiser, template picking, micrograph junk detector, particle pick inspection.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1-cuda12) / Software - details: patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio from blob picking
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1-cuda12) / Number images used: 487566
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1-cuda12)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1-cuda12)
FSC plot (resolution estimation)

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