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- EMDB-72206: Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-72206
TitleCryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
Map datasharpened map
Sample
  • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab4 Fab.
    • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer.
      • Protein or peptide: BG505 SOSIP.664 gp41
      • Protein or peptide: BG505 SOSIP.664 gp120
    • Complex: Rhesus macaque Ab4
      • Protein or peptide: Ab 4 Fab heavy chain
      • Protein or peptide: Ab 4 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 / VIRAL PROTEIN-IMMUNE SYSTEM complex
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: 3.01 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 Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
Authors: Chandravanshi M / Tolbert WD / Pazgier M
History
DepositionAug 19, 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_72206.png

Downloads & links

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Map

FileDownload / File: emd_72206.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368.52 Å		0.92 Å/pix.
x 400 pix.
= 368.52 Å		0.92 Å/pix.
x 400 pix.
= 368.52 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: 0.155
Minimum - Maximum-1.9493506 - 2.6922174
Average (Standard dev.)0.0004448413 (±0.044550024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_72206_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_72206_half_map_2.map
Annotationhalf map A
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 Ab4 Fab.
Components
  • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer in complex with PGT121 Fab and Rhesus macaque Ab4 Fab.
    • Complex: BG505 SOSIP.664 HIV envelope glycoprotein trimer.
      • Protein or peptide: BG505 SOSIP.664 gp41
      • Protein or peptide: BG505 SOSIP.664 gp120
    • Complex: Rhesus macaque Ab4
      • Protein or peptide: Ab 4 Fab heavy chain
      • Protein or peptide: Ab 4 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 Ab4 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 Ab4

SupramoleculeName: Rhesus macaque Ab4 / 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 gp41

MacromoleculeName: BG505 SOSIP.664 gp41 / type: protein_or_peptide / ID: 1 / 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 #2: BG505 SOSIP.664 gp120

MacromoleculeName: BG505 SOSIP.664 gp120 / type: protein_or_peptide / ID: 2 / 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 #3: Ab 4 Fab heavy chain

MacromoleculeName: Ab 4 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.43824 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLQLQESGPG LVKPSETLSV TCDVSGGSIS DNFWIWIRQA PGQGLEWIGY MYGTNGGTNV NPSFKGRVTL SADTSKNQLS LKVDSVTVA DTAVYYCVRY WNRWGTGYFD YWGQGVLVTV SSASTKGPSV FPLAPSSRST SESTAALGCL VKDYFPEPVT V SWNSGSLT ...String:
QLQLQESGPG LVKPSETLSV TCDVSGGSIS DNFWIWIRQA PGQGLEWIGY MYGTNGGTNV NPSFKGRVTL SADTSKNQLS LKVDSVTVA DTAVYYCVRY WNRWGTGYFD YWGQGVLVTV SSASTKGPSV FPLAPSSRST SESTAALGCL VKDYFPEPVT V SWNSGSLT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYVCNVNH KPSNTKVDKR VEIKTCGGGS K

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Macromolecule #4: Ab 4 Fab light chain

MacromoleculeName: Ab 4 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.666242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAVVTQEPSM TVSPGGTVTL TCASSTGAVA IGHTPHWFQQ KPGQVPRALI YHSDQKHSGT PARFSGSLLG DKAALTLSGA LPEDEAEYY CWLAFSSGGV FGSGTKLTVL GQPKASPLVT LFPPSSEELQ ANKATLVCLI SDFYPGVVKV AWKADGNSVN T GVETTTPS ...String:
QAVVTQEPSM TVSPGGTVTL TCASSTGAVA IGHTPHWFQQ KPGQVPRALI YHSDQKHSGT PARFSGSLLG DKAALTLSGA LPEDEAEYY CWLAFSSGGV FGSGTKLTVL GQPKASPLVT LFPPSSEELQ ANKATLVCLI SDFYPGVVKV AWKADGNSVN T GVETTTPS KQSNNKYAAS SYLSLTSDQW KSHKSYSCQV THEGSTVEKT VAPTECS

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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 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 21 / 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

Concentration1.60 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Chloride
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate
1.8 mMKH2PO4Potassium Phosphate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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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: 2392293
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7uoj

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 436694
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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