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- PDB-9y7n: HCMV Protease in complex with Fab5 - Class 3 -

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Basic information

Entry
Database: PDB / ID: 9y7n
TitleHCMV Protease in complex with Fab5 - Class 3
Components
  • Assemblin
  • Fab5 Heavy Chain
  • Fab5 light chain
KeywordsHYDROLASE / Cytomegalovirus / protease / antibody / complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZimanyi, M. / Hulce, K.R. / Bohn, M.F. / Norman, J. / Rohweder, P.J. / Detomasi, T.C. / Cheng, Y. / Craik, C.
Funding support United States, 2items
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, K.R. / Bohn, M.F. / Norman, J. / Rohweder, P.J. / Cheng, Y. / Craik, C.
History
DepositionSep 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Assemblin
B: Fab5 Heavy Chain
C: Fab5 light chain


Theoretical massNumber of molelcules
Total (without water)78,0033
Polymers78,0033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Assemblin / Protease / Pr


Mass: 29089.678 Da / Num. of mol.: 1 / Mutation: A143V, A209V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytomegalovirus / Gene: UL80, APNG / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P16753, assemblin
#2: Antibody Fab5 Heavy Chain


Mass: 24942.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Antibody Fab5 light chain


Mass: 23970.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
Has protein modificationY

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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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Complex of Fab5 and human cytomegalovirus proteaseCOMPLEXFab fragment isolated from fully human naive phage-displayed libraryall0RECOMBINANT
2Fab5COMPLEX#2-#31RECOMBINANT
3Human cytomegalovirus proteaseCOMPLEX#11RECOMBINANT
4Fab5 heavy chainCOMPLEX#22RECOMBINANT
5Fab5 light chainCOMPLEX#32RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
44
55
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cytomegalovirus10358
32Homo sapiens (human)9606
43Cytomegalovirus10358
54Homo sapiens (human)9606
65Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562BL21
32Escherichia coli (E. coli)562BL21
43Escherichia coli (E. coli)562BL21
54Escherichia coli (E. coli)562BL21
65Escherichia coli (E. coli)562BL21
Buffer solutionpH: 8
Details: 25 mM potassium phosphate, 150 mM potassium chloride, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMpotassium chlorideKCl1
225 mMpotassium phosphateK2HPO41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4538
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 6 eV
Image scansWidth: 8192 / Height: 8192

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.1-cuda12particle selectionblob picker first, ab initio reconstruction, then used map for template picking
2SerialEMimage acquisition
4cryoSPARC4.7.1-cuda12CTF correctionpatch CTF
7Cootmodel fitting
9PHENIXmodel refinement
10ISOLDEmodel refinement
11cryoSPARC4.7.1-cuda12initial Euler assignment
12cryoSPARC4.7.1-cuda12final Euler assignment
14cryoSPARC4.7.1-cuda123D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2820568
Details: All in cryoSPARC: Patch motion correction, patch CTF, micrograph denoiser, template picking, micrograph junk detector, particle pick inspection.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 487566 / Symmetry type: POINT
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033656
ELECTRON MICROSCOPYf_angle_d0.5034965
ELECTRON MICROSCOPYf_dihedral_angle_d4.567522
ELECTRON MICROSCOPYf_chiral_restr0.043543
ELECTRON MICROSCOPYf_plane_restr0.004646

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