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- PDB-44ab: PC-Int1 + 13H11-Fab + 2C12-Fab + 7I13-Fab -

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Basic information

Entry
Database: PDB / ID: 44ab
TitlePC-Int1 + 13H11-Fab + 2C12-Fab + 7I13-Fab
Components
  • 13H11 heavy chain
  • 13H11 light chain
  • 2C12 Heavy chain
  • 2C12 Light chain
  • 7I13 Heavy chain
  • 7I13 Light chain
  • UL128
  • UL130
  • UL131A
  • gH
  • gL
KeywordsVIRAL PROTEIN / Virus / Antibody
Biological speciesHuman betaherpesvirus 5
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu, T.C. / Liu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-guided stabilization of the HCMV pentamer enhances thermostability and neutralizing antibody responses
Authors: Liu, P. / Yu, J.P. / Liu, T.C. / Liu, Y. / Wang, X.X.
History
DepositionJul 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / 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: gH
B: gL
C: UL128
D: UL130
E: UL131A
H: 7I13 Heavy chain
L: 7I13 Light chain
P: 2C12 Heavy chain
Q: 2C12 Light chain
X: 13H11 heavy chain
Y: 13H11 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,69017
Polymers254,36311
Non-polymers1,3276
Water00
1


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

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Components

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Protein , 5 types, 5 molecules ABCDE

#1: Protein gH


Mass: 84404.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Production host: Homo sapiens (human)
#2: Protein gL


Mass: 30845.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Production host: Homo sapiens (human)
#3: Protein UL128


Mass: 19777.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Production host: Homo sapiens (human)
#4: Protein UL130


Mass: 24773.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Production host: Homo sapiens (human)
#5: Protein UL131A


Mass: 15011.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Production host: Homo sapiens (human)

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Antibody , 6 types, 6 molecules HLPQXY

#6: Antibody 7I13 Heavy chain


Mass: 13740.323 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 7I13 Light chain


Mass: 11548.807 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 2C12 Heavy chain


Mass: 17723.137 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 2C12 Light chain


Mass: 11916.170 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 13H11 heavy chain


Mass: 13380.985 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 13H11 light chain


Mass: 11241.583 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, 6 molecules

#12: 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.: 6 / 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 pentamer in complex with 3Fabs / Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT
Source (natural)Organism: Human betaherpesvirus 5
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.35
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 564374 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315811
ELECTRON MICROSCOPYf_angle_d0.55121494
ELECTRON MICROSCOPYf_dihedral_angle_d4.6722178
ELECTRON MICROSCOPYf_chiral_restr0.0412438
ELECTRON MICROSCOPYf_plane_restr0.0042742

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