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- EMDB-42366: Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A0... -

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Basic information

Entry
Database: EMDB / ID: EMD-42366
TitleCryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 and PGDM1400 Fabs
Map datasharpened EM volume
Sample
  • Complex: Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A06 and PGDM1400 Fabs
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: PGDM1400 Fab Light Chain
    • Protein or peptide: 04_A06 Fab Heavy Chain
    • Protein or peptide: PGDM1400 Fab Heavy Chain
    • Protein or peptide: 04_A06 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / ANTIBODY / CD4-BINDING SITE / IMMUNE COMPLEX / Viral Protein-Immune System complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDeLaitsch AT / Bjorkman PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002143 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 PGDM1400 Fabs
Authors: DeLaitsch AT / Bjorkman PJ
History
DepositionOct 16, 2023-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42366.png

Downloads & links

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Map

FileDownload / File: emd_42366.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened EM volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.24011804 - 0.42810732
Average (Standard dev.)0.0010487486 (±0.017372975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 346.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42366_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_42366_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened EM volume

Fileemd_42366_additional_1.map
Annotationunsharpened EM volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened EM volume after subtraction of PGDM1400 Fab...

Fileemd_42366_additional_2.map
Annotationsharpened EM volume after subtraction of PGDM1400 Fab and N160 glycans -- C3 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map "A"

Fileemd_42366_half_map_1.map
Annotationhalf map "A"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map "B"

Fileemd_42366_half_map_2.map
Annotationhalf map "B"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A0...

EntireName: Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A06 and PGDM1400 Fabs
Components
  • Complex: Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A06 and PGDM1400 Fabs
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: PGDM1400 Fab Light Chain
    • Protein or peptide: 04_A06 Fab Heavy Chain
    • Protein or peptide: PGDM1400 Fab Heavy Chain
    • Protein or peptide: 04_A06 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A0...

SupramoleculeName: Antibody-antigen complex of HIV-1 BG505 SOSIPv2 trimer with 04_A06 and PGDM1400 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.864086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MI RSENITN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQAFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: PGDM1400 Fab Light Chain

MacromoleculeName: PGDM1400 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.093719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DFVLTQSPHS LSVTPGESAS ISCKSSHSLI HGDRNNYLAW YVQKPGRSPQ LLIYLASSRA SGVPDRFSGS GSDKDFTLKI SRVETEDVG TYYCMQGRES PWTFGQGTKV DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DFVLTQSPHS LSVTPGESAS ISCKSSHSLI HGDRNNYLAW YVQKPGRSPQ LLIYLASSRA SGVPDRFSGS GSDKDFTLKI SRVETEDVG TYYCMQGRES PWTFGQGTKV DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #4: 04_A06 Fab Heavy Chain

MacromoleculeName: 04_A06 Fab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.690879 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVRLDQSGTA VKKPGASVRV SCRAPDSFTV YRPRLSAYFI GEFNIHWLRQ APGQGLEWLG FVNIFRGAVK YSSRFQGRIT ITRDTSSET SYLDLGALKA DDTATYYCAW DKNVDDNPWR LDSWGQGTLV IVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
SVRLDQSGTA VKKPGASVRV SCRAPDSFTV YRPRLSAYFI GEFNIHWLRQ APGQGLEWLG FVNIFRGAVK YSSRFQGRIT ITRDTSSET SYLDLGALKA DDTATYYCAW DKNVDDNPWR LDSWGQGTLV IVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK TH HHHHH

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Macromolecule #5: PGDM1400 Fab Heavy Chain

MacromoleculeName: PGDM1400 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.526812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAQLVQSGPE VRKPGTSVKV SCKAPGNTLK TYDLHWVRSV PGQGLQWMGW ISHEGDKKVI VERFKAKVTI DWDRSTNTAY LQLSGLTSG DTAVYYCAKG SKHRLRDYAL (TYS)DDDGALNWA VDVDYLSNLE FWGQGTAVTV SSASTKGPSV FPLAPSS KS TSGGTAALGC ...String:
QAQLVQSGPE VRKPGTSVKV SCKAPGNTLK TYDLHWVRSV PGQGLQWMGW ISHEGDKKVI VERFKAKVTI DWDRSTNTAY LQLSGLTSG DTAVYYCAKG SKHRLRDYAL (TYS)DDDGALNWA VDVDYLSNLE FWGQGTAVTV SSASTKGPSV FPLAPSS KS TSGGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVD K RVEPKSCDKT HHHHHH

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Macromolecule #6: 04_A06 Fab Light Chain

MacromoleculeName: 04_A06 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.142639 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YIQVTQSPSS LSASIGDTIT VACEVSQDVG WAVNWYHQRP GRPPYNLIYT AHNLAPGVAS RFRGSRVGTY FTLTINNLLP EDVGTYYCQ VFDSFAPGGT RVDLRGTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES V TEQDSKDS ...String:
YIQVTQSPSS LSASIGDTIT VACEVSQDVG WAVNWYHQRP GRPPYNLIYT AHNLAPGVAS RFRGSRVGTY FTLTINNLLP EDVGTYYCQ VFDSFAPGGT RVDLRGTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN ALQSGNSQES V TEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.02 MTris-HClTris
0.15 MNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blot, 0 blot force.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2446 / Average exposure time: 1.8 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 46972
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6udj

source_name: PDB, initial_model_type: experimental model

8uki

source_name: PDB, initial_model_type: experimental model

4rqq

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ulu:
Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 and PGDM1400 Fabs

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