[English] 日本語
![](img/lk-miru.gif)
- EMDB-7125: Recombinant major vault protein [Rattus norvegicus] structure in ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-7125 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Recombinant major vault protein [Rattus norvegicus] structure in solution: conformation 2 | ||||||||||||||||||||||||||||||
![]() | |||||||||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||||||||
![]() | Vault Recombinant protein structure Engineered nano-particle / STRUCTURAL PROTEIN | ||||||||||||||||||||||||||||||
Function / homology | ![]() protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||||||||||||||||||||
![]() | Ding K / Zhang X | ||||||||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||||||||
![]() | ![]() Title: Solution Structures of Engineered Vault Particles. Authors: Ke Ding / Xing Zhang / Jan Mrazek / Valerie A Kickhoefer / Mason Lai / Hwee L Ng / Otto O Yang / Leonard H Rome / Z Hong Zhou / ![]() Abstract: Prior crystal structures of the vault have provided clues of its structural variability but are non-conclusive due to crystal packing. Here, we obtained vaults by engineering at the N terminus of rat ...Prior crystal structures of the vault have provided clues of its structural variability but are non-conclusive due to crystal packing. Here, we obtained vaults by engineering at the N terminus of rat major vault protein (MVP) an HIV-1 Gag protein segment and determined their near-atomic resolution (∼4.8 Å) structures in a solution/non-crystalline environment. The barrel-shaped vaults in solution adopt two conformations, 1 and 2, both with D39 symmetry. From the N to C termini, each MVP monomer has three regions: body, shoulder, and cap. While conformation 1 is identical to one of the crystal structures, the shoulder in conformation 2 is translocated longitudinally up to 10 Å, resulting in an outward-projected cap. Our structures clarify the structural discrepancies in the body region in the prior crystallography models. The vault's drug-delivery potential is highlighted by the internal disposition and structural flexibility of its Gag-loaded N-terminal extension at the barrel waist of the engineered vault. | ||||||||||||||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 2.5 GB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 164.9 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bp7MC ![]() 7126C ![]() 6bp8C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Major vault protein [Rattus norvegicus]
Entire | Name: Major vault protein [Rattus norvegicus] |
---|---|
Components |
|
-Supramolecule #1: Major vault protein [Rattus norvegicus]
Supramolecule | Name: Major vault protein [Rattus norvegicus] / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Major vault protein
Macromolecule | Name: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 103.931305 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTPRTLNAWV KVVEEKAFSP EVIPMFTALS EGATPSDLNT MLNTIGGHQA AMQMLKDTIN EEAAEWDRGF LGLMATEEAI IRIPPYHYI HVLDQNSNVS RVEVGPKTYI RQDNERVLFA PVRMVTVPPR HYCIVANPVS RDTQSSVLFD ITGQVRLRHA D QEIRLAQD ...String: MTPRTLNAWV KVVEEKAFSP EVIPMFTALS EGATPSDLNT MLNTIGGHQA AMQMLKDTIN EEAAEWDRGF LGLMATEEAI IRIPPYHYI HVLDQNSNVS RVEVGPKTYI RQDNERVLFA PVRMVTVPPR HYCIVANPVS RDTQSSVLFD ITGQVRLRHA D QEIRLAQD PFPLYPGEVL EKDITPLQVV LPNTALHLKA LLDFEDKNGD KVMAGDEWLF EGPGTYIPQK EVEVVEIIQA TV IKQNQAL RLRARKECFD REGKGRVTGE EWLVRSVGAY LPAVFEEVLD LVDAVILTEK TALHLRALQN FRDLRGVLHR TGE EWLVTV QDTEAHVPDV YEEVLGVVPI TTLGPRHYCV ILDPMGPDGK NQLGQKRVVK GEKSFFLQPG ERLERGIQDV YVLS EQQGL LLKALQPLEE GESEEKVSHQ AGDCWLIRGP LEYVPSAKVE VVEERQAIPL DQNEGIYVQD VKTGKVRAVI GSTYM LTQD EVLWEKELPS GVEELLNLGH DPLADRGQKG TAKPLQPSAP RNKTRVVSYR VPHNAAVQVY DYRAKRARVV FGPELV TLD PEEQFTVLSL SAGRPKRPHA RRALCLLLGP DFFTDVITIE TADHARLQLQ LAYNWHFELK NRNDPAEAAK LFSVPDF VG DACKAIASRV RGAVASVTFD DFHKNSARII RMAVFGFEMS EDTGPDGTLL PKARDQAVFP QNGLVVSSVD VQSVEPVD Q RTRDALQRSV QLAIEITTNS QEAAAKHEAQ RLEQEARGRL ERQKILDQSE AEKARKELLE LEAMSMAVES TGNAKAEAE SRAEAARIEG EGSVLQAKLK AQALAIETEA ELERVKKVRE MELIYARAQL ELEVSKAQQL ANVEAKKFKE MTEALGPGTI RDLAVAGPE MQVKLLQSLG LKSTLITDGS SPINLFSTAF GLLGLGSDGQ PPAQK UniProtKB: Major vault protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 32.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9669 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |