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Yorodumi- EMDB-23571: Cryo-EM structure of ConM SOSIP.v7 (ConM) in complex with bNAb PGT122 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23571 | |||||||||
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Title | Cryo-EM structure of ConM SOSIP.v7 (ConM) in complex with bNAb PGT122 | |||||||||
Map data | filtered and B-factor sharpened map | |||||||||
Sample |
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Keywords | Env / SOSIP / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
Authors | Martin GM / Ward AB | |||||||||
Funding support | 1 items
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Citation | Journal: NPJ Vaccines / Year: 2023 Title: Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens. Authors: Gregory M Martin / Rebecca A Russell / Philip Mundsperger / Scarlett Harris / Lu Jovanoska / Luiza Farache Trajano / Torben Schiffner / Katalin Fabian / Monica Tolazzi / Gabriella Scarlatti ...Authors: Gregory M Martin / Rebecca A Russell / Philip Mundsperger / Scarlett Harris / Lu Jovanoska / Luiza Farache Trajano / Torben Schiffner / Katalin Fabian / Monica Tolazzi / Gabriella Scarlatti / Leon McFarlane / Hannah Cheeseman / Yoann Aldon / Edith E Schermer / Marielle Breemen / Kwinten Sliepen / Dietmar Katinger / Renate Kunert / Rogier W Sanders / Robin Shattock / Andrew B Ward / Quentin J Sattentau / Abstract: Chemical cross-linking is used to stabilize protein structures with additional benefits of pathogen and toxin inactivation for vaccine use, but its use has been restricted by the potential for local ...Chemical cross-linking is used to stabilize protein structures with additional benefits of pathogen and toxin inactivation for vaccine use, but its use has been restricted by the potential for local or global structural distortion. This is of particular importance when the protein in question requires a high degree of structural conservation for inducing a biological outcome such as the elicitation of antibodies to conformationally sensitive epitopes. The HIV-1 envelope glycoprotein (Env) trimer is metastable and shifts between different conformational states, complicating its use as a vaccine antigen. Here we have used the hetero-bifunctional zero-length reagent 1-Ethyl-3-(3-Dimethylaminopropyl)-Carbodiimide (EDC) to cross-link two soluble Env trimers, selected well-folded trimer species using antibody affinity, and transferred this process to good manufacturing practice (GMP) for experimental medicine use. Cross-linking enhanced trimer stability to biophysical and enzyme attack. Cryo-EM analysis revealed that cross-linking retained the overall structure with root-mean-square deviations (RMSDs) between unmodified and cross-linked Env trimers of 0.4-0.5 Å. Despite this negligible distortion of global trimer structure, we identified individual inter-subunit, intra-subunit, and intra-protomer cross-links. Antigenicity and immunogenicity of the trimers were selectively modified by cross-linking, with cross-linked ConS retaining bnAb binding more consistently than ConM. Thus, the EDC cross-linking process improves trimer stability whilst maintaining protein folding, and is readily transferred to GMP, consistent with the more general use of this approach in protein-based vaccine design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23571.map.gz | 5.9 MB | EMDB map data format | |
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Header (meta data) | emd-23571-v30.xml emd-23571.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_23571.png | 56.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23571 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23571 | HTTPS FTP |
-Validation report
Summary document | emd_23571_validation.pdf.gz | 427 KB | Display | EMDB validaton report |
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Full document | emd_23571_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | emd_23571_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_23571_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23571 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23571 | HTTPS FTP |
-Related structure data
Related structure data | 7lxmMC 7lx2C 7lx3C 7lxnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23571.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | filtered and B-factor sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.026 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ConM SOSIP.v7 in complex with bNAb PGT122
Entire | Name: ConM SOSIP.v7 in complex with bNAb PGT122 |
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Components |
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-Supramolecule #1: ConM SOSIP.v7 in complex with bNAb PGT122
Supramolecule | Name: ConM SOSIP.v7 in complex with bNAb PGT122 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: ConM SOSIP.v7
Supramolecule | Name: ConM SOSIP.v7 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Supramolecule #3: PGT122 Fab
Supramolecule | Name: PGT122 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: HIV-1 Env glycoprotein gp120
Macromolecule | Name: HIV-1 Env glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 55.897863 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYDTEK RNVWATHCCV PTDPNPQEI VLENVTENFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLNCTDV NATNNTTNNE EIKNCSFNIT T ELRDKKKK ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYDTEK RNVWATHCCV PTDPNPQEI VLENVTENFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLNCTDV NATNNTTNNE EIKNCSFNIT T ELRDKKKK VYALFYKLDV VPIDDNNSYR LINCNTSAIT QACPKVSFEP IPIHYCAPAG FAILKCNDKK FNGTGPCKNV ST VQCTHGI KPVVSTQLLL NGSLAEEEII IRSENITNNA KTIIVQLNES VEINCTRPNN NTRKSIRIGP GQWFYATGDI IGD IRQAHC NISRTKWNKT LQQVAKKLRE HFNKTIIFNP SSGGDLEITT HSFNCGGEFF YCNTSELFNS TWNGTNNTIT LPCR IKQII NMWQRVGQAM YAPPIEGKIR CTSNITGLLL TRDGGNNNTE TFRPGGGDMR DNWRSELYKY KVVKIEPLGV APTRC KRRV VERRRRRRA |
-Macromolecule #2: HIV-1 Env glycoprotein gp41
Macromolecule | Name: HIV-1 Env glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 17.214486 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEC QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSQD EIWDNMTWME WDKEINNYTD IIYSLIEESQ NQQEKNEQEL LALD |
-Macromolecule #3: PGT122 Fab heavy chain
Macromolecule | Name: PGT122 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.434691 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC |
-Macromolecule #4: PGT122 Fab light chain
Macromolecule | Name: PGT122 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.880275 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ ...String: APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ SNNKYAASSY LSLTPEQWKS HKSYSCQVTH EGSTVEKTVA PTECS |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144741 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |