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- EMDB-41810: Cryo-EM structure of vaccine-elicited CD4 binding site antibody D... -

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Basic information

Entry
Database: EMDB / ID: EMD-41810
TitleCryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env Local Refinement
Map dataLocally refined map showing the vaccine elicited DH1285 antibody fab bound to one of pg120 protomer of CH505M5chimer.6R.SOSIP.664v4.1 Env
Sample
  • Complex: The complex of vaccine elicited CD4 binding site neutralizing antibody DH1285 Fab with CH505M5chimer.6R.SOSIP.664v4.1 Env
    • Complex: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: DH1285 Heavy Chain, DH1285 Light Chain
      • Protein or peptide: DH1285 Heavy Chain
      • Protein or peptide: DH1285 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Vaccine induced neutralizing antibody / CD4 binding site antibody / gp120 / DH1285 / IgG / rhesus macaques / CH505M5chimer.6R.SOSIP.664v4.1 Env / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsThakur B / Stalls VD / Acharya P
Funding support United States, 2 items
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, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41810.png

Downloads & links

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Map

FileDownload / File: emd_41810.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally refined map showing the vaccine elicited DH1285 antibody fab bound to one of pg120 protomer of CH505M5chimer.6R.SOSIP.664v4.1 Env
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.45709625 - 0.8383502
Average (Standard dev.)-0.0003744583 (±0.012465785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41810_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41810_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of vaccine elicited CD4 binding site neutralizing ant...

EntireName: The complex of vaccine elicited CD4 binding site neutralizing antibody DH1285 Fab with CH505M5chimer.6R.SOSIP.664v4.1 Env
Components
  • Complex: The complex of vaccine elicited CD4 binding site neutralizing antibody DH1285 Fab with CH505M5chimer.6R.SOSIP.664v4.1 Env
    • Complex: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: DH1285 Heavy Chain, DH1285 Light Chain
      • Protein or peptide: DH1285 Heavy Chain
      • Protein or peptide: DH1285 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The complex of vaccine elicited CD4 binding site neutralizing ant...

SupramoleculeName: The complex of vaccine elicited CD4 binding site neutralizing antibody DH1285 Fab with CH505M5chimer.6R.SOSIP.664v4.1 Env
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: One of the gp120 protomer bound to DH1285 locally refined to get precise information about the interacting residues.
Molecular weightTheoretical: 308 KDa

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Supramolecule #2: Envelope glycoprotein gp120

SupramoleculeName: Envelope glycoprotein gp120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: DH1285 Heavy Chain, DH1285 Light Chain

SupramoleculeName: DH1285 Heavy Chain, DH1285 Light Chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Details: CH505M5chimer.6R.SOSIP.664v4.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 72.669078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNM WKNDMVDQMH EDVISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA L FYKLDIVQ ...String:
MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNM WKNDMVDQMH EDVISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA L FYKLDIVQ LDGNSSQYRL INCNTSVITQ ACPKVSFDPI PIHYCAPAGY AILKCNNKTF TGTGPCNNVS TVQCTHGIKP VV STQLLLN GSLAEGEIII RSENITNNVK TIIVHLNESV KIECTRPNNK TRTSIRIGPG QWFYATGQVI GDIREAYCNI NES KWNETL QRVSKKLKEY FPHKNITFQP SSGGDLEITT HSFNCGGEFF YCNTSSLFNR TYMANSTDMA NSTETNSTRT ITIH CRIKQ IINMWQEVGR AMYAPPIAGN ITCISNITGL LLTRDGGKNN TETFRPGGGN MKDNWRSELY KYKVVKIEPL GVAPT RCKR RVVGRRRRRR AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQ ARV LAVERYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNE QD LLALD

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Macromolecule #2: DH1285 Heavy Chain

MacromoleculeName: DH1285 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.396316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAM TRDRSTTTAY MDLSSLTSED TAVYYCARDE GGSGSYSYFD SWGQGVLVTV SSASTKGPSV FPLAPSSRST S ESTAALGC ...String:
MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAM TRDRSTTTAY MDLSSLTSED TAVYYCARDE GGSGSYSYFD SWGQGVLVTV SSASTKGPSV FPLAPSSRST S ESTAALGC LVKDYFPEPV TVSWNSGSLT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYVCNVNH KPSNTKVDKR VE IKT

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Macromolecule #3: DH1285 Light Chain

MacromoleculeName: DH1285 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.240955 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTD YTLTISSLQP EDFATYYCQH YSTSPYTFGR GTKVDIKRAV AAPSVFIFPP SEDQVKSGTV SVVCLLNNFY P REASVKWK ...String:
MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTD YTLTISSLQP EDFATYYCQH YSTSPYTFGR GTKVDIKRAV AAPSVFIFPP SEDQVKSGTV SVVCLLNNFY P REASVKWK VDGVLKTGNS QESVTEQDSK DNTYSLSSTL TLSSTDYQSH NVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 14427340
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 146444

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8u1d:
Cryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env Local Refinement

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