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- PDB-9pzc: HCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K... -

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Basic information

Entry
Database: PDB / ID: 9pzc
TitleHCMV trimer in complex with G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K Fabs
Components
  • (Envelope glycoprotein ...) x 2
  • (Immunoglobulin heavy variable 1- ...) x 2
  • (Immunoglobulin heavy variable 4- ...) x 2
  • (Immunoglobulin kappa variable ...) x 2
  • A12K Fab heavy chain
  • A12K Fab light chain
  • B5L Fab light chain
  • C4K Fab heavy chain
  • C4K Fab light chain
  • C5K Fab light chain
  • G1L Fab heavy chain
  • Immunoglobulin lambda variable 1-51
KeywordsVIRAL PROTEIN / Virus / glycoprotein / antibody
Function / homology
Function and homology information


monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation ...monomeric IgA immunoglobulin complex / pentameric IgM immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / immunoglobulin complex / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / FCERI mediated NF-kB activation / antibacterial humoral response / blood microparticle / Potential therapeutics for SARS / host cell Golgi apparatus / adaptive immune response / entry receptor-mediated virion attachment to host cell / immune response / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / : / extracellular exosome / extracellular region / plasma 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 / : / : ...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 / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin kappa variable 1-39 / Immunoglobulin kappa variable 3-20 / Immunoglobulin lambda variable 1-51 / Immunoglobulin heavy variable 1-46 / Immunoglobulin heavy variable 4-39 / Immunoglobulin heavy variable 4-34 / 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

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Immunoglobulin lambda variable 1-51
D: G1L Fab heavy chain
E: Immunoglobulin heavy variable 1-46
F: Immunoglobulin kappa variable 3-20
G: A12K Fab heavy chain
H: Immunoglobulin heavy variable 4-34
I: A12K Fab light chain
J: Immunoglobulin kappa variable 1-39
K: Immunoglobulin heavy variable 4-39
L: B5L Fab light chain
M: C5K Fab light chain
N: Immunoglobulin heavy variable 1-46
O: C4K Fab heavy chain
P: C4K Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,06819
Polymers289,40416
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
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
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 CDEFGHIJKLMNOP

#3: Antibody Immunoglobulin lambda variable 1-51 / Ig lambda chain V-I region BL2 / Ig lambda chain V-I region EPS / Ig lambda chain V-I region NEW / ...Ig lambda chain V-I region BL2 / Ig lambda chain V-I region EPS / Ig lambda chain V-I region NEW / Ig lambda chain V-I region NIG-64


Mass: 11542.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV1-51 / Production host: Homo sapiens (human) / References: UniProt: P01701
#4: Antibody G1L Fab heavy chain


Mass: 13754.686 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 Immunoglobulin heavy variable 1-46 / Ig heavy chain V-I region DOT / Ig heavy chain V-I region HG3 / Ig heavy chain V-I region Mot


Mass: 13243.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV1-46 / Production host: Homo sapiens (human) / References: UniProt: P01743
#6: Antibody Immunoglobulin kappa variable 3-20 / Ig kappa chain V-III region B6 / Ig kappa chain V-III region GOL / Ig kappa chain V-III region HAH ...Ig kappa chain V-III region B6 / Ig kappa chain V-III region GOL / Ig kappa chain V-III region HAH / Ig kappa chain V-III region HIC / Ig kappa chain V-III region IARC/BL41 / Ig kappa chain V-III region NG9 / Ig kappa chain V-III region SIE / Ig kappa chain V-III region Ti / Ig kappa chain V-III region WOL


Mass: 11560.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKV3-20 / Production host: Homo sapiens (human) / References: UniProt: P01619
#7: Antibody A12K Fab heavy chain


Mass: 12971.682 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 Immunoglobulin heavy variable 4-34 / Ig heavy chain V-II region ARH-77


Mass: 13668.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV4-34 / Production host: Homo sapiens (human) / References: UniProt: P06331
#9: Antibody A12K Fab light chain


Mass: 11702.073 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 Immunoglobulin kappa variable 1-39 / Ig kappa chain V-I region DEE / Ig kappa chain V-I region Hau / Ig kappa chain V-I region Mev / Ig ...Ig kappa chain V-I region DEE / Ig kappa chain V-I region Hau / Ig kappa chain V-I region Mev / Ig kappa chain V-I region OU / Ig kappa chain V-I region Walker


Mass: 11678.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKV1-39 / Production host: Homo sapiens (human) / References: UniProt: P01597
#11: Antibody Immunoglobulin heavy variable 4-39 / Ig heavy chain V-II region WAH


Mass: 13333.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV4-39 / Production host: Homo sapiens (human) / References: UniProt: P01824
#12: Antibody B5L Fab light chain


Mass: 11503.529 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 C5K Fab light chain


Mass: 11824.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#14: Antibody Immunoglobulin heavy variable 1-46 / Ig heavy chain V-I region DOT / Ig heavy chain V-I region HG3 / Ig heavy chain V-I region Mot


Mass: 13339.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV1-46 / Production host: Homo sapiens (human) / References: UniProt: P01743
#15: Antibody C4K Fab heavy chain


Mass: 13167.801 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 C4K Fab light chain


Mass: 11697.043 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 G1L (II), G1L (A), B5L, C4K, B1K, A7K, A12K, and C5K 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: 92567 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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