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- PDB-9pzb: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F... -

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Basic information

Entry
Database: PDB / ID: 9pzb
TitleHCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
Components
  • (Envelope glycoprotein ...) x 2
  • A9K Fab heavy chain
  • A9K Fab light chain
  • B1K Fab heavy chain
  • B1K Fab light chain
  • E10L Fab heavy chain
  • E10L Fab light chain
  • E4K Fab heavy chain
  • E4K Fab light chain
  • E8K Fab heavy chaun
  • E8K Fab light chain
  • E9L Fab heavy chaun
  • E9L Fab light chain
  • F12L Fab heavy chain
  • F12L Fab light chain
KeywordsVIRAL PROTEIN / Virus / glycoprotein / antibody
Function / homology
Function and homology information


host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain
Similarity search - Domain/homology
Envelope glycoprotein H / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Structural characterization of antibodies for synergistic HCMV neutralization
Authors: Ashurov, A. / Goldsmith, J.A. / McLellan, J.S. / Zehner, M. / Klein, F.
History
DepositionAug 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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: Envelope glycoprotein H
B: Envelope glycoprotein L
D: E10L Fab light chain
E: E10L Fab heavy chain
F: A9K Fab heavy chain
G: A9K Fab light chain
H: E8K Fab heavy chaun
I: E8K Fab light chain
J: F12L Fab heavy chain
K: F12L Fab light chain
L: E9L Fab light chain
M: E9L Fab heavy chaun
N: B1K Fab heavy chain
O: B1K Fab light chain
P: E4K Fab heavy chain
Q: E4K Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,33319
Polymers290,66916
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein H


Mass: 84538.617 Da / Num. of mol.: 1 / Mutation: A13T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Gene: UL75 / Production host: Homo sapiens (human) / References: UniProt: Q69155
#2: Protein Envelope glycoprotein L / gL


Mass: 29877.336 Da / Num. of mol.: 1 / Mutation: K41E,G77R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Gene: UL115, gL, HHV5gp102 / Production host: Homo sapiens (human) / References: UniProt: Q8JP80

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Antibody , 14 types, 14 molecules DEFGHIJKLMNOPQ

#3: Antibody E10L Fab light chain


Mass: 11679.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody E10L Fab heavy chain


Mass: 13452.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody A9K Fab heavy chain


Mass: 12993.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody A9K Fab light chain


Mass: 11597.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: Antibody E8K Fab heavy chaun


Mass: 14369.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#8: Antibody E8K Fab light chain


Mass: 12477.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#9: Antibody F12L Fab heavy chain


Mass: 12956.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#10: Antibody F12L Fab light chain


Mass: 12438.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#11: Antibody E9L Fab light chain


Mass: 11461.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#12: Antibody E9L Fab heavy chaun


Mass: 13016.661 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#13: Antibody B1K Fab heavy chain


Mass: 12984.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#14: Antibody B1K Fab light chain


Mass: 11566.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#15: Antibody E4K Fab heavy chain


Mass: 13517.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#16: Antibody E4K Fab light chain


Mass: 11741.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 3 molecules

#17: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
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

ComponentName: HCMV trimer in complex with E4K, E11K, A9K, E9L, E8K, B1K, E7K, F12L and E10L Fabs
Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT
Source (natural)Organism: Human betaherpesvirus 5
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141765 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319884
ELECTRON MICROSCOPYf_angle_d0.58427049
ELECTRON MICROSCOPYf_dihedral_angle_d6.1522809
ELECTRON MICROSCOPYf_chiral_restr0.0443010
ELECTRON MICROSCOPYf_plane_restr0.0053464

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