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- PDB-8u1d: Cryo-EM structure of vaccine-elicited CD4 binding site antibody D... -

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Basic information

Entry
Database: PDB / ID: 8u1d
TitleCryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env Local Refinement
Components
  • DH1285 Heavy Chain
  • DH1285 Light Chain
  • Envelope glycoprotein gp120
KeywordsVIRAL PROTEIN / HIV-1 Vaccine induced neutralizing antibody / CD4 binding site antibody / gp120 / DH1285 / IgG / rhesus macaques / CH505M5chimer.6R.SOSIP.664v4.1 Env
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsThakur, B. / Stalls, V.D. / Acharya, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144371 United States
CitationJournal: To be published
Title: Rhesus macaque vaccine elicited antibody DH1285 Fab bound to the one of the gp120 promoter of CH505M5chimer.6R.SOSIP.664v4.1 Env
Authors: Thakur, B. / Acharya, P.
History
DepositionAug 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp120
I: DH1285 Heavy Chain
J: DH1285 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5284
Polymers124,3063
Non-polymers2211
Water0
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 Envelope glycoprotein gp120 /


Mass: 72669.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CH505M5chimer.6R.SOSIP.664v4.1 / Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Antibody DH1285 Heavy Chain


Mass: 26396.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Antibody DH1285 Light Chain


Mass: 25240.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
Has ligand of interestN

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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
IDNameTypeDetailsEntity IDParent-IDSource
1The complex of vaccine elicited CD4 binding site neutralizing antibody DH1285 Fab with CH505M5chimer.6R.SOSIP.664v4.1 EnvCOMPLEXOne of the gp120 protomer bound to DH1285 locally refined to get precise information about the interacting residues.#1-#30RECOMBINANT
2Envelope glycoprotein gp120COMPLEX#11RECOMBINANT
3DH1285 Heavy Chain, DH1285 Light ChainCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.308 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Human immunodeficiency virus 111676
23Macaca mulatta (Rhesus monkey)9544
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 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 FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 59.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14427340
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146444 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055222
ELECTRON MICROSCOPYf_angle_d1.0097085
ELECTRON MICROSCOPYf_dihedral_angle_d6.258710
ELECTRON MICROSCOPYf_chiral_restr0.058789
ELECTRON MICROSCOPYf_plane_restr0.008908

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