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- EMDB-27622: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1 Trimer, 2-Fab-bound configuration | |||||||||
![]() | Sharp map from homogeneous C1 refinement in cryosparc | |||||||||
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Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Stalls V / Achyara P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rhesus macaque vaccine elicited antibody DH1285 bound to HIV-1 Env trimer Authors: Stalls V / Acharya P | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
Images | ![]() | 44.6 KB | ||
Others | ![]() ![]() | 115.6 MB 115.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharp map from homogeneous C1 refinement in cryosparc | ||||||||||||||||||||
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: Half B map from homogeneous C1 refinement in cryosparc
File | emd_27622_half_map_1.map | ||||||||||||
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Annotation | Half B map from homogeneous C1 refinement in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half A map from homogeneous C1 refinement in cryosparc
File | emd_27622_half_map_2.map | ||||||||||||
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Annotation | Half A map from homogeneous C1 refinement in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI...
Entire | Name: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration |
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Components |
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-Supramolecule #1: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI...
Supramolecule | Name: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 308 KDa |
-Macromolecule #1: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer
Macromolecule | Name: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL FYKLDIVQLD ...String: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL FYKLDIVQLD GNSSQYRLIN CNTSVITQAC PKVSFDPIPI HYCAPAGYAI LKCNNKTFTG TGPCNNVSTV QCTHGIKPVV STQLLLNGSL AEGEIIIRSE NITNNVKTII VHLNESVKIE CTRPNNKTRT SIRIGPGQWF YATGQVIGDI REAYCNINES KWNETLQRVS KKLKEYFPHK NITFQPSSGG DLEITTHSFN CGGEFFYCNT SSLFNRTYMA NSTDMANSTE TNSTRTITIH CRIKQIINMW QEVGRAMYAP PIAGNITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRRAVGIGA VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR APEAQQHLLK LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKLICCTN VPWNSSWSNR NLSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: DH1285 Fab Heavy Chain
Macromolecule | Name: DH1285 Fab Heavy Chain / type: other / ID: 2 / Classification: other |
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Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | String: MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAMT RDRSTTTAYM DLSSLTSEDT AVYYCARDEG GSGSYSYFDS WGQGVLVTVS SASTKGPSVF PLAPSSRSTS ESTAALGCLV ...String: MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAMT RDRSTTTAYM DLSSLTSEDT AVYYCARDEG GSGSYSYFDS WGQGVLVTVS SASTKGPSVF PLAPSSRSTS ESTAALGCLV KDYFPEPVTV SWNSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKT |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #3: DH1285 Fab Light Chain
Macromolecule | Name: DH1285 Fab Light Chain / type: other / ID: 3 / Classification: other |
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Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | String: MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTDY TLTISSLQPE DFATYYCQHY STSPYTFGRG TKVDIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD ...String: MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTDY TLTISSLQPE DFATYYCQHY STSPYTFGRG TKVDIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD GVLKTGNSQE SVTEQDSKDN TYSLSSTLTL SSTDYQSHNV YACEVTHQGL SSPVTKSFNR GEC |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.1 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 4146196 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 78101 |
-Atomic model buiding 1
Refinement | Space: REAL |
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