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- EMDB-48059: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOM... -

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Basic information

Entry
Database: EMDB / ID: EMD-48059
TitleStructure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I
Map data
Sample
  • Complex: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I
    • Protein or peptide: HIV-1 BG505 SOSIP gp41
    • Protein or peptide: HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120
    • Protein or peptide: 10-1074 Fab Heavy Chain
    • Protein or peptide: 10-1074 Fab Light Chain
    • Protein or peptide: IOMAmin5 Fab Heavy Chain
    • Protein or peptide: IOMAmin5 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Env / bNAb / 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 / 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDam KA / Yang Z / Bjorkman PJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 United States
Bill & Melinda Gates FoundationCAVD INV-002143 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U54 AI170856 United States
CitationJournal: Cell Rep / Year: 2025
Title: Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design.
Authors: Kim-Marie A Dam / Harry B Gristick / Yancheng E Li / Zhi Yang / Priyanthi N P Gnanapragasam / Anthony P West / Michael S Seaman / Pamela J Bjorkman /
Abstract: HIV-1 broadly neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA class of CD4bs ...HIV-1 broadly neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA class of CD4bs bNAbs includes fewer rare features and somatic hypermutations (SHMs) to achieve broad neutralization, thus presenting a potentially accessible pathway for vaccine-induced bNAb development. Here, we created a library of IOMA variants in which each SHM was individually reverted to the inferred germline counterpart to investigate the roles of SHMs in conferring IOMA's neutralization potency and breadth. Impacts on neutralization for each variant were evaluated, and this information was used to design minimally mutated IOMA-class variants (IOMAmin) that incorporated the fewest SHMs required for achieving IOMA's neutralization breadth. A cryoelectron microscopy (cryo-EM) structure of an IOMAmin variant bound to Env was used to further interpret characteristics of IOMA variants to elucidate how IOMA's structural features correlate with its neutralization mechanism, informing the design of IOMA-targeting immunogens.
History
DepositionNov 23, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48059.png

Downloads & links

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Map

FileDownload / File: emd_48059.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 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: 0.000283
Minimum - Maximum-0.011172708 - 0.028072674
Average (Standard dev.)0.00010592322 (±0.0008684954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48059_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_48059_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOM...

EntireName: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I
Components
  • Complex: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I
    • Protein or peptide: HIV-1 BG505 SOSIP gp41
    • Protein or peptide: HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120
    • Protein or peptide: 10-1074 Fab Heavy Chain
    • Protein or peptide: 10-1074 Fab Light Chain
    • Protein or peptide: IOMAmin5 Fab Heavy Chain
    • Protein or peptide: IOMAmin5 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOM...

SupramoleculeName: Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #5-#6, #3-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120

MacromoleculeName: HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.518332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPAGAGSNLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEIH LENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT TELRDKKQKV Y SLFYRLDV ...String:
MDAMKRGLCC VLLLCGAVFV SPAGAGSNLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEIH LENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT TELRDKKQKV Y SLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NGTGPCPSVS TV QCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAFYATGDII GDI RQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWISNTSVQ GSNS TGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYK VVKI EPLGVAPTRC KRRVVGRRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: HIV-1 BG505 SOSIP gp41

MacromoleculeName: HIV-1 BG505 SOSIP 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: IOMAmin5 Fab Heavy Chain

MacromoleculeName: IOMAmin5 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.347196 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAQ VKKPGASVTV SCTASGYTFT GYHMHWVRQA PGQGLEWMGW INPFRGGVKY AQKFRGRVSM TRDTSIEIFY MELSRLRSD DTAVYYCARE MFDSSADWSP WRGMVAWGQG TLVTVSSAS

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Macromolecule #4: IOMAmin5 Fab Light Chain

MacromoleculeName: IOMAmin5 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.540678 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGSSRDVG GFDLVSWYQQ HPGKAPKLMI YEVSKRPSGV SNRFSASKSG NTASLTISGL QAEDEADYY CYSYADGVAF GGGTKLTVLG QP

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Macromolecule #5: 10-1074 Fab Heavy Chain

MacromoleculeName: 10-1074 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.878512 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSAS

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Macromolecule #6: 10-1074 Fab Light Chain

MacromoleculeName: 10-1074 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.089441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
YVRPLSVALG ETARISCGRQ ALGSRAVQWY QHRPGQAPIL LIYNNQDRPS GIPERFSGTP DINFGTRATL TISGVEAGDE ADYYCHMWD SRSGFSWSFG GATRLTVLGQ P

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 27 / 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 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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

Particle selectionNumber selected: 860116
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t3x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 78720
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ehl:
Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I

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