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- EMDB-26648: The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-26648
TitleThe CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664
Map dataPhenix sharpened map.
Sample
  • Complex: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: N49-P9.6-FR3 Fab heavy chain
    • Protein or peptide: N49-P9.6-FR3 Fab light chain
    • Protein or peptide: PGT121 Fab light chain
    • Protein or peptide: PGT121 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / envelope trimer / GP120 / GP41 / viral entry / type-1 membrane fusion glycoprotein / N49P9.6-FR3 / PGT121 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma 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 speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsNguyen DN / 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)R01AI147870 United States
CitationJournal: To Be Published
Title: The structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP
Authors: Nguyen DN / Tolbert WD / Pazgier M
History
DepositionApr 13, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26648.png

Downloads & links

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Map

FileDownload / File: emd_26648.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhenix sharpened map.
Voxel sizeX=Y=Z: 1.38953 Å
Density
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-48.407800000000002 - 49.328429999999997
Average (Standard dev.)0.000000000004753 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B used to generate sharpened map.

Fileemd_26648_half_map_1.map
AnnotationHalf map B used to generate sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A used to generate sharpened map.

Fileemd_26648_half_map_2.map
AnnotationHalf map A used to generate sharpened 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 : One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fab...

EntireName: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
Components
  • Complex: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: N49-P9.6-FR3 Fab heavy chain
    • Protein or peptide: N49-P9.6-FR3 Fab light chain
    • Protein or peptide: PGT121 Fab light chain
    • Protein or peptide: PGT121 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fab...

SupramoleculeName: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: Fab fragments were generated from papain digest of their respective IgGs. Each component was purified separately. Components were mixed and the complex was purified by gel filtration.
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 / Details: Env mimic BG505 SOSIP.664 / 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: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Details: Env mimic BG505 SOSIP.664 / 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: N49-P9.6-FR3 Fab heavy chain

MacromoleculeName: N49-P9.6-FR3 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.024129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HVQLVQSGGG VKKIGAAVRI SCEVSGYNFM DQFINWVRQA PGQGLEWMGW MNPIYGQVNY SWRFQGRVTM TRQLSQDPDD PDWGTAFME LRGLRVDDTA VYYCARGPSG ENYPFHYWGQ GVRVVVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
HVQLVQSGGG VKKIGAAVRI SCEVSGYNFM DQFINWVRQA PGQGLEWMGW MNPIYGQVNY SWRFQGRVTM TRQLSQDPDD PDWGTAFME LRGLRVDDTA VYYCARGPSG ENYPFHYWGQ GVRVVVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK SC

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Macromolecule #4: N49-P9.6-FR3 Fab light chain

MacromoleculeName: N49-P9.6-FR3 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.733291 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LTQPASMSAS PGQSVTISCS GTRHIISAWF QQYPGKPPKL IIFDDDKRPS GVPSRFSASR PGDTASLTIS NVQPEDEATY ICNTYEFFG GGTKLTVLGQ PKAAPSVTLF PPSSEELQAN KATLVCLVSD FYPGAVTVAW KADGSPVKVG VETTKPSKQS N NKYAASSY ...String:
LTQPASMSAS PGQSVTISCS GTRHIISAWF QQYPGKPPKL IIFDDDKRPS GVPSRFSASR PGDTASLTIS NVQPEDEATY ICNTYEFFG GGTKLTVLGQ PKAAPSVTLF PPSSEELQAN KATLVCLVSD FYPGAVTVAW KADGSPVKVG VETTKPSKQS N NKYAASSY LSLTPEQWKS HRSYSCRVTH EGSTVEKTVA PAECS

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Macromolecule #5: PGT121 Fab light chain

MacromoleculeName: PGT121 Fab light chain / type: protein_or_peptide / ID: 5 / 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 #6: PGT121 Fab heavy chain

MacromoleculeName: PGT121 Fab heavy chain / type: protein_or_peptide / ID: 6 / 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 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 15 / 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

BufferpH: 7.2 / Details: Phosphate buffered saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsQuantifoil R1.2/1.3

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4368 / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

DetailsData sets from two grid types were combined into a single data set.
Particle selectionNumber selected: 3151423
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6cdi


Details: 6CDI was used for the BG505 SOSIP.664, 5CEZ was used for the PGT121 Fab, and 7SX7 was used for the N49-P9.6-FR3 Fab.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 132055
Initial angle assignmentType: OTHER / Software - Name: UCSF ChimeraX
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: PHENIX
Final 3D classificationNumber classes: 1 / Avg.num./class: 132055 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

6cdi

chain_id: G, residue_range: 31-505, source_name: PDB, initial_model_type: experimental model

6cdi

chain_id: A, residue_range: 31-505, source_name: PDB, initial_model_type: experimental model

6cdi

chain_id: I, residue_range: 31-505, source_name: PDB, initial_model_type: experimental model

6cdi

chain_id: B, residue_range: 513-664, source_name: PDB, initial_model_type: experimental model

6cdi

chain_id: C, residue_range: 513-664, source_name: PDB, initial_model_type: experimental model

6cdi

chain_id: J, residue_range: 513-664, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: h, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: d, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: k, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: l, residue_range: 6-107, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: e, residue_range: 6-107, source_name: PDB, initial_model_type: experimental model

5cez

chain_id: m, residue_range: 6-107, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: H, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: D, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: K, residue_range: 1-112, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: L, residue_range: 3-107, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: E, residue_range: 3-107, source_name: PDB, initial_model_type: experimental model

7sx7

chain_id: M, residue_range: 3-107, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7uoj:
The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664

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