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Yorodumi- EMDB-41440: Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trim... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41440 | |||||||||
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Title | Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibody / Vaccination / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.03 Å | |||||||||
Authors | Roark RS / Morano NC / 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_41440.map.gz | 106.7 MB | EMDB map data format | |
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Header (meta data) | emd-41440-v30.xml emd-41440.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_41440.png | 113.1 KB | ||
Filedesc metadata | emd-41440.cif.gz | 5.9 KB | ||
Others | emd_41440_half_map_1.map.gz emd_41440_half_map_2.map.gz | 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41440 | HTTPS FTP |
-Validation report
Summary document | emd_41440_validation.pdf.gz | 978.3 KB | Display | EMDB validaton report |
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Full document | emd_41440_full_validation.pdf.gz | 977.9 KB | Display | |
Data in XML | emd_41440_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_41440_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41440 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41440 | HTTPS FTP |
-Related structure data
Related structure data | 8to9MC 8tdxC 8tnuC 8to7C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41440.map.gz / Format: CCP4 / Size: 216 MB / 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41440_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41440_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
Entire | Name: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP |
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Components |
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-Supramolecule #1: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
Supramolecule | Name: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP 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: Homo sapiens (human) |
Molecular weight | Theoretical: 52.737102 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NLWVTVYYGV PVWKEAKTTL FCASDAKAYE KEVHNVWATH ACVPTDPNPQ EMVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC TNVNVTNTNN NNMKEEMKNC SFNTTTEIRD KKQKEYALFY RLDIVPLNEN SSEYRLINCN T STITQICP ...String: NLWVTVYYGV PVWKEAKTTL FCASDAKAYE KEVHNVWATH ACVPTDPNPQ EMVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC TNVNVTNTNN NNMKEEMKNC SFNTTTEIRD KKQKEYALFY RLDIVPLNEN SSEYRLINCN T STITQICP KVSFDPIPIH YCAPAGYAIL KCNNKTFNGT GPCNNVSTVQ CTHGIKPVVS TQLLLNGSLA EEEIIIRSEN LT DNAKTII VHLNESVEIN CTRPNNMTRK SIRIGPGQTF YALGDIIGDI RQPHCNISEA KWNKTLQRVK KKLKEHFPNK TIK FAPSSG GDLEITTHSF NCRGEFFYCN TSKLFNSTYN NTTSNSTITL PCRIKQIINM WQEVGRAMYA PPIAGNITCK SNIT GLLLT RDGGNNNNNT ETFRPGGGDM RDNWRSELYK YKVVEIKPLG IAPTKCKRRV VERRRRRR |
-Macromolecule #2: TRNM-f*01 heavy chain
Macromolecule | Name: TRNM-f*01 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
Molecular weight | Theoretical: 13.923301 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG VVKPSETLSL TCAVSGDSIK SAYQYWNWIR QPRGKGPEWI GGVYSSSDST AYNPSLESRV SISRDTSNNR FSLNLRSVT ATDTATYFCA RSVRDSRGWG RYFLDTWGQG LLVTVSS |
-Macromolecule #3: TRNM-f*01 light chain
Macromolecule | Name: TRNM-f*01 light 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: 11.464811 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDTVT ITCRASQSIS TWLAWYQQKP GKAPKVLIYS ASILQSGVPS RFRGSGSGSD FTLTIGSLQI EDFATYFCQ QYTGSPFTFG GGTKVEIK |
-Macromolecule #4: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.174447 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGLGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTAVPW NSSWSNKSQE DIWDNMTWMQ WDREIGNYTD TIYRLLEESQ FQQEINEKDL LALD |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / 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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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: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97698 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |