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Yorodumi- EMDB-23149: Cryo-electron microscopy reconstruction of antibody DH898.1 Fab-d... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23149 | |||||||||
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Title | Cryo-electron microscopy reconstruction of antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env SOSIP trimer CH848 10.17 | |||||||||
Map data | Final sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Edwards RJ / Acharya P | |||||||||
Funding support | United States, 2 items
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Citation | Journal: bioRxiv / Year: 2020 Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N ...Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N / Perfect J / Moody MA / Wiehe K / Bradley T / Kepler TB / Alam SM / Foulger A / Bonsignori M / LaBranche CC / Montefiori DC / Seaman M / Santra S / Francica JR / Lynn GM / Aussedat B / Walkowicz WE / Laga R / Kelso G / Saunders KO / Fera D / Kwong PD / Seder RA / Bartesaghi A / Shaw GM / Acharya P / Haynes BF | |||||||||
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_23149.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-23149-v30.xml emd-23149.xml | 29.3 KB 29.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23149_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_23149.png | 108.1 KB | ||
Masks | emd_23149_msk_1.map emd_23149_msk_2.map | 64 MB 64 MB | Mask map | |
Others | emd_23149_additional_1.map.gz emd_23149_additional_2.map.gz emd_23149_half_map_1.map.gz emd_23149_half_map_2.map.gz | 31.4 MB 6.1 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23149 | HTTPS FTP |
-Validation report
Summary document | emd_23149_validation.pdf.gz | 518.2 KB | Display | EMDB validaton report |
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Full document | emd_23149_full_validation.pdf.gz | 517.8 KB | Display | |
Data in XML | emd_23149_validation.xml.gz | 15.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23149 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23149 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0665 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23149_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_23149_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unmodified final map of antibody DH898.1 Fab-dimer bound...
File | emd_23149_additional_1.map | ||||||||||||
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Annotation | Unmodified final map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local resolution ofof antibody DH898.1 Fab-dimer bound to...
File | emd_23149_additional_2.map | ||||||||||||
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Annotation | Local resolution ofof antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer, at the 0.5 FSC level. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A of antibody DH898.1 Fab-dimer bound to...
File | emd_23149_half_map_1.map | ||||||||||||
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Annotation | Half-map A of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B of antibody DH898.1 Fab-dimer bound to...
File | emd_23149_half_map_2.map | ||||||||||||
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Annotation | Half-map B of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV...
Entire | Name: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer |
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Components |
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-Supramolecule #1: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV...
Supramolecule | Name: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 94 KDa |
-Supramolecule #2: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
Supramolecule | Name: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: CH848 10.17 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293F |
-Supramolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) dimer
Supramolecule | Name: Antibody DH898.1 Fragment antigen binding (Fab) dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Composed of two heavy chains and two light chains |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293F |
-Macromolecule #1: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664
Macromolecule | Name: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: CH848.3.D0949.10.17 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV ...String: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV TFEPIPIHYC APAGYAILKC NDETFNGTGP CSNVSTVQCT HGIRPVVSTQ LLLNGSLAEK EIVIRSENLT NNAKIIIVHL HTPVEIVCTR PNNNTRKSVR IGPGQTFYAT GDIIGDIKQA HCNISEEKWN DTLQKVGIEL QKHFPNKTIK YNQSAGGDME ITTHSFNCGG EFFYCNTSNL FNGTYNGTYI STNSSANSTS TITLQCRIKQ IINMWQGVGR CMYAPPIAGN ITCRSNITGL LLTRDGGTNS NETETFRPAG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR RAVGIGAVFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQSNLLRAPE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #2: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain
Macromolecule | Name: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) / Strain: DH898.1 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV ...String: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVE |
-Macromolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) light chain
Macromolecule | Name: Antibody DH898.1 Fragment antigen binding (Fab) light chain type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) / Strain: DH898.1 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE ...String: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE QDSKDNTYSL SSTLTLSNTD YQSHNVYACE VTHQGLSSPV TKSFNRGE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP Details: 2.5 microliter of smaple applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane. | |||||||||
Details | For the DH898.1-bound complex, purified HIV-1 Env was mixed with 6-fold molar excess of recombinantly expressed and purified DH898.1 Fab to obtain a final Env concentration of 1.5 mg/ml, and incubated for 2 hours at room temperature. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3230 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |