[English] 日本語
![](img/lk-miru.gif)
- EMDB-21383: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-21383 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 | |||||||||
![]() | Sharpened map | |||||||||
![]() |
| |||||||||
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 / immune response / 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 / immune response / 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 / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Gorman J / Kwong PD | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition. Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping ...Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping Yang / Baoshan Zhang / Nicole A Doria-Rose / Bob Lin / Penny L Moore / Lynn Morris / Lawrence Shapiro / John R Mascola / Peter D Kwong / ![]() ![]() Abstract: Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate ...Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate diverse modes of Env recognition typified by antibodies of the PG9 class and the PGT145 class. The mode of recognition, however, has been unclear for the most potent of the V1V2 apex-targeting antibodies, CAP256-VRC26.25 (named for donor-lineage.clone and referred to hereafter as VRC26.25). Here, we determine the cryoelectron microscopy structure at 3.7 Å resolution of the antigen-binding fragment of VRC26.25 in complex with the Env trimer thought to have initiated the lineage. The 36-residue protruding loop of VRC26.25 displays recognition incorporating both strand-C interactions similar to the PG9 class and V1V2 apex insertion similar to the PGT145 class. Structural elements of separate antibody classes can thus intermingle to form a "combined" class, which in this case yields an antibody of extraordinary potency. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 108.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 25.1 KB 25.1 KB | Display Display | ![]() |
Images | ![]() | 79 KB | ||
Masks | ![]() | 115.9 MB | ![]() | |
Others | ![]() ![]() ![]() | 23.4 MB 107.6 MB 107.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 809.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 808.7 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vttMC ![]() 6vrwC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map
File | emd_21383_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A
File | emd_21383_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map B
File | emd_21383_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime...
Entire | Name: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime...
Supramolecule | Name: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
---|
-Supramolecule #2: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
Supramolecule | Name: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: CAP256-VRC26.25 Fab
Supramolecule | Name: CAP256-VRC26.25 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|---|
Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.322434 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI ...String: GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEEEIIIRS EN LTDNVKT IIVHLNESVE ITCTRPNNMT RKSVRIGPGQ TFYALGDIIG DIRQPHCNIS EIKWEKTLQR VSEKLREHFN KTI IFNQSS GGDLEITTHS FNCGGEFFYC NTSDLFFNKT FNETYSTGSN STNSTITLPC RIKQIINMWQ EVGRAMYAPP IAGN ITCKS NITGLLLTRD GGGNNSTKET FRPGGGNMRD NWRSELYKYK VVEVKPLGIA PTECNRTVVQ RRRRRR |
-Macromolecule #2: VRC26.25 Heavy Chain
Macromolecule | Name: VRC26.25 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.083482 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGKQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP ...String: QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGKQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNH KPSNT KVDKRVEPKS CDKGLEVLFQ |
-Macromolecule #3: VRC26.25 Light Chain
Macromolecule | Name: VRC26.25 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.052611 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QSVLTQPPSV SAAPGQKVTI SCSGNTSNIG NNFVSWYQQR PGRAPQLLIY ETDKRPSGIP DRFSASKSGT SGTLAITGLQ TGDEADYYC ATWAASLSSA RVFGTGTKVI VLVQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String: QSVLTQPPSV SAAPGQKVTI SCSGNTSNIG NNFVSWYQQR PGRAPQLLIY ETDKRPSGIP DRFSASKSGT SGTLAITGLQ TGDEADYYC ATWAASLSSA RVFGTGTKVI VLVQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS |
-Macromolecule #4: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.355703 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVVGLGAVFL GFLGAAGSTM GAASNTLTVQ ARQLLSGIVQ QQSNLLRAPE AQQHMLQLGV WGFKQLQARV LAIERYLEVQ QLLGMWGCS GKLICCTNVP WNSSWSNKTY NEIWDNMTWM QWDREIGNYT DTIYKLLEVS QFQQEINEKD NLTLD |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 41 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7.4 / Component - Formula: PBS |
Grid | Model: C-flat-1.2/1.3 4C / 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 |
Details | Cryo-EM Structure of Fab CAP256-VRC26.25 bound to HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2 |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1777 / Average exposure time: 10.0 sec. / Average electron dose: 64.48 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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |