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Yorodumi- EMDB-27624: Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27624 | |||||||||
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Title | Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab | |||||||||
Map data | Cryosparc generated map; Z-flip | |||||||||
Sample |
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Keywords | HIV-1 Env / VIRAL PROTEIN / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
Authors | Gobeil S / Acharya P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques Authors: Gobeil SM / Janowska K / Stalls V / Mansouri K / Henderson RC / Edwards RJ / Wiehe K / Saunders K / Acharya P / Williams W / Haynes BF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27624.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-27624-v30.xml emd-27624.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_27624.png | 98 KB | ||
Filedesc metadata | emd-27624.cif.gz | 6.5 KB | ||
Others | emd_27624_half_map_1.map.gz emd_27624_half_map_2.map.gz | 115.4 MB 115.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27624 | HTTPS FTP |
-Validation report
Summary document | emd_27624_validation.pdf.gz | 745 KB | Display | EMDB validaton report |
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Full document | emd_27624_full_validation.pdf.gz | 744.5 KB | Display | |
Data in XML | emd_27624_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_27624_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27624 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27624 | HTTPS FTP |
-Related structure data
Related structure data | 8dowMC 8dp1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27624.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryosparc generated map; Z-flip | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryosparc generated half map A
File | emd_27624_half_map_1.map | ||||||||||||
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Annotation | Cryosparc generated half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc generated half map B
File | emd_27624_half_map_2.map | ||||||||||||
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Annotation | Cryosparc generated half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
Entire | Name: HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab |
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Components |
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-Supramolecule #1: HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
Supramolecule | Name: HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
-Macromolecule #1: Envelope glycoprotein gp120
Macromolecule | Name: Envelope 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: 51.736535 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDATVKTG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP ...String: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDATVKTG TVEEMKNCSF NTTTEIRDKE KKEYALFYKP DIVPLSETNN TSEYRLINCN T SACTQACP KVTFEPIPIH YCAPAGYAIL KCNDETFNGT GPCSNVSTVQ CTHGIRPVVS TQLLLNGSLA EKEIVIRSEN LT NNAKIII VHLHTPVEIV CTRPNNNTRK SVRIGPGQTF YATGDIIGDI KQAHCNISEE KWNDTLQKVG IELQKHFPNK TIK YNQSAG GDMEITTHSF NCGGEFFYCN TSNLFNGTYN GTYISTNSSA NSTSTITLQC RIKQIINMWQ GVGRCMYAPP IAGN ITCRS NITGLLLTRD GGTNSNETET FRPAGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRV UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: Envelope glycoprotein gp41
Macromolecule | Name: Envelope 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 / Strain: BG505 |
Molecular weight | Theoretical: 18.24583 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VGRRRRRRAV GIGAVFLGFL GAAGSTMGAA SMTLTVQARN LLSGIVQQQS NLLRAPEAQQ HLLKLTVWGI KQLQARVLAV ERYLRDQQL LGIWGCSGKL ICCTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA L D UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: DH1030.1 Fab Heavy chain
Macromolecule | Name: DH1030.1 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 24.947818 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLAESGGG LTKPGGSLRL SCAASGFTFS DFYMDWVRQT PGKGLEWVSR INNDGRNKWY ADSVRGRFTV SRENAKNTLY LQMDSLRAE DTAVYYCARD RPVYRYWSGG YHLDPWGQGV VVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String: EVQLAESGGG LTKPGGSLRL SCAASGFTFS DFYMDWVRQT PGKGLEWVSR INNDGRNKWY ADSVRGRFTV SRENAKNTLY LQMDSLRAE DTAVYYCARD RPVYRYWSGG YHLDPWGQGV VVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIKTC GG |
-Macromolecule #4: DH1030.1 Fab Light Chain
Macromolecule | Name: DH1030.1 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 24.050713 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: YVVMTQSPLS LPITPGQPAS ISCRSSQRLL HSDGNTYLAW YQQRPGQPPR RLIYEVSKLD SGVPDRFSGS GAGTDFTLKI SRVEAEDVG VYYCGQNTYL PYSFGQGSKV EIKRAVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGVL K TGNSQESV ...String: YVVMTQSPLS LPITPGQPAS ISCRSSQRLL HSDGNTYLAW YQQRPGQPPR RLIYEVSKLD SGVPDRFSGS GAGTDFTLKI SRVEAEDVG VYYCGQNTYL PYSFGQGSKV EIKRAVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGVL K TGNSQESV TEQDSKDNTY SLSSTLTLSN TDYQSHNVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 18 / 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
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: CH848 10.17DT Env - PDB ID: 6UM6 DH1030.1 Fab crystal structure - PDB ID: 8DKF |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296846 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |