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Yorodumi- EMDB-41438: Cryo-EM structure of HERH-b*01 Fab in complex with HIV-1 Env trim... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41438 | |||||||||
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Title | Cryo-EM structure of HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibody / Vaccination / VIRAL PROTEIN / IMMUNE SYSTEM / 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 / apoptotic process / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.39 Å | |||||||||
Authors | Roark RS / Hoyt F / Hansen B / Fischer E / Shapiro LS / Kwong PD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques Authors: Wang H / Kwong PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41438.map.gz | 848.6 MB | EMDB map data format | |
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Header (meta data) | emd-41438-v30.xml emd-41438.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_41438.png | 115.1 KB | ||
Filedesc metadata | emd-41438.cif.gz | 6.3 KB | ||
Others | emd_41438_half_map_1.map.gz emd_41438_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41438 | HTTPS FTP |
-Validation report
Summary document | emd_41438_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41438_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41438_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | emd_41438_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41438 | HTTPS FTP |
-Related structure data
Related structure data | 8to7MC 8tdxC 8tnuC 8to9C 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_41438.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.42 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41438_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41438_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
Entire | Name: HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP |
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Components |
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-Supramolecule #1: HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
Supramolecule | Name: HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Surface protein gp120, Transmembrane protein gp41
Supramolecule | Name: Surface protein gp120, Transmembrane protein gp41 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Supramolecule #3: HERH-b*01 heavy chain, HERH-b*01 light chain
Supramolecule | Name: HERH-b*01 heavy chain, HERH-b*01 light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
-Macromolecule #1: Surface protein gp120
Macromolecule | Name: Surface protein 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: 54.086324 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 SACTQACPKV 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 CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: Transmembrane protein gp41
Macromolecule | Name: Transmembrane protein 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: 17.146482 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: HERH-b*01 heavy chain
Macromolecule | Name: HERH-b*01 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: 25.558494 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSETLSL TCGVSGDSIT RNYYYWHWIR QSPGKGLEGL GYIAYTGGTD YSPSFKSRVT ISRDTSKNQF SLKLTSVTV ADTAVYFCAR ERGDSYIYSY DGVDFWGQGL LVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String: QVQLQESGPG LVKPSETLSL TCGVSGDSIT RNYYYWHWIR QSPGKGLEGL GYIAYTGGTD YSPSFKSRVT ISRDTSKNQF SLKLTSVTV ADTAVYFCAR ERGDSYIYSY DGVDFWGQGL LVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIKTC GGLEVLFQGP |
-Macromolecule #4: HERH-b*01 light chain
Macromolecule | Name: HERH-b*01 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: 23.998727 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DAVLTQSPLS LPITPGEPAS ISCRSSQSLL HTNGETYLNW YQQKTGQRPR LLISQVSKRE IGVPDRFSAS GAGSDFTLKI SRVEAEDVG LYFCGQGLHW PRTFGQGTRV DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String: DAVLTQSPLS LPITPGEPAS ISCRSSQSLL HTNGETYLNW YQQKTGQRPR LLISQVSKRE IGVPDRFSAS GAGSDFTLKI SRVEAEDVG LYFCGQGLHW PRTFGQGTRV DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 45 / 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: 7.5 / Details: PBS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 562633 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |