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- EMDB-72094: Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-72094
TitleCryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
Map data
Sample
  • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab76 Fab.
    • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer.
      • Protein or peptide: BG505 SOSIP.664 gp120
      • Protein or peptide: BG505 SOSIP.664 gp41
    • Complex: Rhesus macaque Ab76
      • Protein or peptide: Ab76 Fab heavy chain
      • Protein or peptide: Ab76 Fab light chain
    • Complex: PGT121 Fab
      • Protein or peptide: PGT121 Fab heavy chain
      • Protein or peptide: PGT121 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Env / Broadly-neutralizing antibodies (bNAbs) / glycan hole / CD4-binding site (CD4bs) / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 / Macaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsChandravanshi M / Tolbert WD / Pazgier M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI174979 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
Authors: Chandravanshi M / Tolbert WD / Pazgier M
History
DepositionAug 12, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72094.png

Downloads & links

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Map

FileDownload / File: emd_72094.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 440 pix.
= 405.372 Å		0.92 Å/pix.
x 440 pix.
= 405.372 Å		0.92 Å/pix.
x 440 pix.
= 405.372 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9213 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.9754069 - 1.7128512
Average (Standard dev.)0.00027912285 (±0.028892023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 405.372 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72094_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_72094_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 : BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with ...

EntireName: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab76 Fab.
Components
  • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab76 Fab.
    • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer.
      • Protein or peptide: BG505 SOSIP.664 gp120
      • Protein or peptide: BG505 SOSIP.664 gp41
    • Complex: Rhesus macaque Ab76
      • Protein or peptide: Ab76 Fab heavy chain
      • Protein or peptide: Ab76 Fab light chain
    • Complex: PGT121 Fab
      • Protein or peptide: PGT121 Fab heavy chain
      • Protein or peptide: PGT121 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with ...

SupramoleculeName: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab76 Fab.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: BG505 SOSIP.664 HIV envelope glycoprotein trimer.

SupramoleculeName: BG505 SOSIP.664 HIV envelope glycoprotein trimer. / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: Rhesus macaque Ab76

SupramoleculeName: Rhesus macaque Ab76 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #4: PGT121 Fab

SupramoleculeName: PGT121 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BG505 SOSIP.664 gp120

MacromoleculeName: BG505 SOSIP.664 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.064277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: BG505 SOSIP.664 gp41

MacromoleculeName: BG505 SOSIP.664 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: Ab76 Fab heavy chain

MacromoleculeName: Ab76 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.511357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVKPGGSLRL SCVASGFSFS SYEMHWVRQA PGKGLEWVSY FSDTGGITYY ADSVKGRFTI SRDNAENSLF LQMNNLRVE DTAVYYCARG GYTGSWIDLF DLWGQGVLVT VSSASTKGPS VFPLAPSSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL ...String:
DVQLVESGGG LVKPGGSLRL SCVASGFSFS SYEMHWVRQA PGKGLEWVSY FSDTGGITYY ADSVKGRFTI SRDNAENSLF LQMNNLRVE DTAVYYCARG GYTGSWIDLF DLWGQGVLVT VSSASTKGPS VFPLAPSSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYVCNVN HKPSNTKVDK RVEIKTCGGG SK

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Macromolecule #4: Ab76 Fab light chain

MacromoleculeName: Ab76 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.473018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KAILTQPASL SASPGASASL TCTFSGGIHV AGYHIFWYQQ KPGSPPRYLL RYKSDSDKAQ GSGVPSRFSG SKDASANTGI LRISGLQSE DEADYYCAIG HSDGHGLFGG GTRLTVLGQP KASPLVTLFP PSSEELQANK ATLVCLISDF YPGVVKVAWK A DGNSVNTG ...String:
KAILTQPASL SASPGASASL TCTFSGGIHV AGYHIFWYQQ KPGSPPRYLL RYKSDSDKAQ GSGVPSRFSG SKDASANTGI LRISGLQSE DEADYYCAIG HSDGHGLFGG GTRLTVLGQP KASPLVTLFP PSSEELQANK ATLVCLISDF YPGVVKVAWK A DGNSVNTG VETTTPSKQS NNKYAASSYL SLTSDQWKSH KSYSCQVTHE GSTVEKTVAP TECS

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Macromolecule #5: PGT121 Fab heavy chain

MacromoleculeName: PGT121 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.16923 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMQLQESGPG LVKPSETLSL TCSVSGASIS DSYWSWIRRS PGKGLEWIGY VHKSGDTNYS PSLKSRVNLS LDTSKNQVSL SLVAATAAD SGKYYCARTL HGRRIYGIVA FNEWFTYFYM DVWGNGTQVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QMQLQESGPG LVKPSETLSL TCSVSGASIS DSYWSWIRRS PGKGLEWIGY VHKSGDTNYS PSLKSRVNLS LDTSKNQVSL SLVAATAAD SGKYYCARTL HGRRIYGIVA FNEWFTYFYM DVWGNGTQVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

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Macromolecule #6: PGT121 Fab light chain

MacromoleculeName: PGT121 Fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.869338 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQIDISVAP GETARISCGE KSLGSRAVQW YQHRAGQAPS LIIYNNQDRP SGIPERFSGS PDSPFGTTAT LTITSVEAGD EADYYCHIW DSRVPTKWVF GGGTTLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
QVQIDISVAP GETARISCGE KSLGSRAVQW YQHRAGQAPS LIIYNNQDRP SGIPERFSGS PDSPFGTTAT LTITSVEAGD EADYYCHIW DSRVPTKWVF GGGTTLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHKSYSCQVT HEGSTVEKTV APTEC

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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: 17 / 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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Chloride
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate
1.8 mMKH2PO4Potassium Phosphate

Details: 1X PBS buffer
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Pressure: 0.00039000000000000005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV
Details0.7 with 0.025% OG

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Particle selectionNumber selected: 5717622
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7uoj

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 332541
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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