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- EMDB-26706: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664 | |||||||||
![]() | sharpened map | |||||||||
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Function / homology | ![]() : / 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 ...: / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
![]() | Gorman J / Kwong PD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664 Authors: Gorman J / Kwong PD | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.1 KB 23.1 KB | Display Display | ![]() |
Images | ![]() | 104.7 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 10 MB 31.9 MB 115.8 MB 115.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ur6MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.083 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Density modified with resolve
File | emd_26706_additional_1.map | ||||||||||||
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Annotation | Density modified with resolve | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_26706_additional_2.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_26706_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_26706_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
Entire | Name: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176 |
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Components |
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-Supramolecule #1: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
Supramolecule | Name: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: gp120
Macromolecule | Name: gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.648887 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA ...String: GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA CTQICPKVTF EPIPIHYCAP AGYAILKCNN KTFNGTGPCN NVSTVQCTHG IKPVVSTQLL LNGSLAEKEI II RSENLTN NAKTIIVHLN ESVGIVCTRP SNMTRKSIRI GPGQTFYALG DIIGDIRQPH CNISKQNWNR TLQQVGRKLA EHF PNRNIT FNHSSGGDLE ITTHSFNCRG EFFYCNTSGL FNGTYHPNGT YNETAVNSSD TITLQCRIKQ IINMWQEVGR CMYA PPIAG NITCNSNITG LLLTRDGGIN QTGEEIFRPG GGDMRDNWRS ELYKYKVVEI KPLGIAPTKC KRRVVERRRR RR |
-Macromolecule #2: gp41
Macromolecule | Name: gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.24051 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTNVPW NSTWSNRTQE DIWNNMTWME WEREIGNYTH TIYSLLEESQ FQQEINEKDL LALD |
-Macromolecule #3: Heavy Chain
Macromolecule | Name: Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.505475 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVTLKESGPA LVKPTQTLTL TCTFSGFSMS NFGSGIYWIR QPPGKALEWL AGIYWTDSKY YNLSLKTRLT ISKDTSKSQV ILIMTNMDP VDTATYYCAD IRGRYYYSNG FLFDVVGVES WGQGVVVTVS S |
-Macromolecule #4: Light Chain
Macromolecule | Name: Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.679873 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QSVLTQPPSA SEAARKTVTI SCSGSRSNIG SNSVSWYKQV PGTAPKLLIK YNDQRPSGVS DRFSGSKSGT SASLAISGLQ TEDEADYYC ATWDDSLNGY IFGVGTRLIV L |
-Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 42 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 1.0 X / Component - Formula: PBS / Component - Name: PBS |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.27 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 13272 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Software - Name: cryoSPARC (ver. 2.12) |