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Yorodumi- EMDB-8573: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8573 | |||||||||
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Title | HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial | |||||||||
Map data | Negative Stain EM Reconstruction of the DH576 Fab in complex with the HIV CH505 SOSIP.664 trimer | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.1 Å | |||||||||
Authors | Fera D / Harrison SC | |||||||||
Citation | Journal: PLoS Pathog / Year: 2017 Title: Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial. Authors: David Easterhoff / M Anthony Moody / Daniela Fera / Hao Cheng / Margaret Ackerman / Kevin Wiehe / Kevin O Saunders / Justin Pollara / Nathan Vandergrift / Rob Parks / Jerome Kim / Nelson L ...Authors: David Easterhoff / M Anthony Moody / Daniela Fera / Hao Cheng / Margaret Ackerman / Kevin Wiehe / Kevin O Saunders / Justin Pollara / Nathan Vandergrift / Rob Parks / Jerome Kim / Nelson L Michael / Robert J O'Connell / Jean-Louis Excler / Merlin L Robb / Sandhya Vasan / Supachai Rerks-Ngarm / Jaranit Kaewkungwal / Punnee Pitisuttithum / Sorachai Nitayaphan / Faruk Sinangil / James Tartaglia / Sanjay Phogat / Thomas B Kepler / S Munir Alam / Hua-Xin Liao / Guido Ferrari / Michael S Seaman / David C Montefiori / Georgia D Tomaras / Stephen C Harrison / Barton F Haynes / Abstract: The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is ...The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody (bnAbs), no plasma bnAb activity was induced. The RV305 (NCT01435135) HIV-1 clinical trial was a placebo-controlled randomized double-blinded study that assessed the safety and efficacy of vaccine boosting on B cell repertoires. HIV-1-uninfected RV144 vaccine recipients were reimmunized 6-8 years later with AIDSVAX B/E gp120 alone, ALVAC-HIV alone, or a combination of ALVAC-HIV and AIDSVAX B/E gp120 in the RV305 trial. Env-specific post-RV144 and RV305 boost memory B cell VH mutation frequencies increased from 2.9% post-RV144 to 6.7% post-RV305. The vaccine was well tolerated with no adverse events reports. While post-boost plasma did not have bnAb activity, the vaccine boosts expanded a pool of envelope CD4 binding site (bs)-reactive memory B cells with long third heavy chain complementarity determining regions (HCDR3) whose germline precursors and affinity matured B cell clonal lineage members neutralized the HIV-1 CRF01 AE tier 2 (difficult to neutralize) primary isolate, CNE8. Electron microscopy of two of these antibodies bound with near-native gp140 trimers showed that they recognized an open conformation of the Env trimer. Although late boosting of RV144 vaccinees expanded a novel pool of neutralizing B cell clonal lineages, we hypothesize that boosts with stably closed trimers would be necessary to elicit antibodies with greater breadth of tier 2 HIV-1 strains. TRIAL REGISTRATION: ClinicalTrials.gov NCT01435135. | |||||||||
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_8573.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-8573-v30.xml emd-8573.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_8573.png | 35.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8573 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8573 | HTTPS FTP |
-Validation report
Summary document | emd_8573_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_8573_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_8573_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8573 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8573 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8573.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative Stain EM Reconstruction of the DH576 Fab in complex with the HIV CH505 SOSIP.664 trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.13 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 : HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w...
Entire | Name: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial |
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Components |
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-Supramolecule #1: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w...
Supramolecule | Name: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293T |
Molecular weight | Theoretical: 50 KDa |
-Supramolecule #2: CH505 Transmitted Founder Envelope
Supramolecule | Name: CH505 Transmitted Founder Envelope / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293T |
-Supramolecule #3: DH576 Fab
Supramolecule | Name: DH576 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 / Details: fab fragment |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293T |
-Macromolecule #1: HIV Envelope
Macromolecule | Name: HIV Envelope / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLN CSNATVDSSK VYDTRSNVNV TSINNTIMGE MKNCSFNTTT EIRDKEKKEY ALFYRPDVVP LDETSNTSEY ...String: VENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLN CSNATVDSSK VYDTRSNVNV TSINNTIMGE MKNCSFNTTT EIRDKEKKEY ALFYRPDVVP LDETSNTSEY RLINCNTSAV TQACPKVTFE PIPIHYCAPA GYAILKCNNK TFNGTGPCSN VSTVQCTHGI RPVVSTQLLL NGSLAEKEIV IRSENLTNNA KIIIVHLNTS VEIVCTRPGN NTRKSVRIGP GQTFYATGDI IGDIRQAHCN ISERQWNKTL QEVGKELQKH FPNKTIKYER SAGGDMEIAT HSFNCGGEFF YCNTSNLFNG TYNGTYISTN STSNITLQCR IKQIINMWQG VGRAMYAPPI AGNITCKSNI TGLLLTRDGG TKNNSNETEE TFRPAGGDMR DNWRSELYKY KVVEIQPLGI APTGCKRRVV GRRRRRRAAG LGALFLGFLG AAGSTMGAAS ITLTVQARQL LSGIVQQQSN LLRAPEAQQH MLQLTVWGIK QLQARVLALE RYLKDQQLLG MWGCSGKLIC CTAVPWNTSW SNKSEKDIWD NMTWMQWERE ISNYTETIYM LLEDSQHQQE RNEKDLLALD |
-Macromolecule #2: DH576 Fab Light Chain
Macromolecule | Name: DH576 Fab Light Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCQASQDID NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGT SFTLTISSLQ PEDIGTYYCQ KYGSVPFPFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK ...String: DIQMTQSPSS LSASVGDRVT ITCQASQDID NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGT SFTLTISSLQ PEDIGTYYCQ KYGSVPFPFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC |
-Macromolecule #3: DH576 Fab Heavy Chain
Macromolecule | Name: DH576 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG VVQPGRSLRL SCGVSGFTFS NYAIHWVRQA PGKRLEWVAL ISYDGKKQYY LDSVKGRFTI SRDNSKDMVY LQMNSLKAED TAIYYCARDR ARSTGYFGGI YYYYYGMDVW GQGTTVTVS GASTKGPSVF PLAPSSKSTS GG TAALGCL VKDYFPEPVT ...String: EVQLVESGGG VVQPGRSLRL SCGVSGFTFS NYAIHWVRQA PGKRLEWVAL ISYDGKKQYY LDSVKGRFTI SRDNSKDMVY LQMNSLKAED TAIYYCARDR ARSTGYFGGI YYYYYGMDVW GQGTTVTVS GASTKGPSVF PLAPSSKSTS GG TAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTY ICNVNH KPSNTKVDKR VEPKSCDKHH HHHH |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: 2% uranyl formate used to stain sample for 20 s | ||||||||||||
Grid | Model: EMS / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Details | HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 22929 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |