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- EMDB-7125: Recombinant major vault protein [Rattus norvegicus] structure in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7125
TitleRecombinant major vault protein [Rattus norvegicus] structure in solution: conformation 2
Map data
Sample
  • Organelle or cellular component: Major vault protein [Rattus norvegicus]
    • Protein or peptide: Major vault protein
KeywordsVault Recombinant protein structure Engineered nano-particle / STRUCTURAL PROTEIN
Function / homology
Function and homology information


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
Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain ...Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsDing K / Zhang X
Funding support United States, 9 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI043203 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106528 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-338135 United States
CitationJournal: Structure / Year: 2018
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
DepositionNov 22, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseApr 4, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bp7
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bp7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7125.png

Downloads & links

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Map

FileDownload / File: emd_7125.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 900 pix.
= 900. Å		1 Å/pix.
x 900 pix.
= 900. Å		1 Å/pix.
x 900 pix.
= 900. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165 / Movie #1: 0.0165
Minimum - Maximum-0.08010286 - 0.059468698
Average (Standard dev.)0.00012398858 (±0.0026799322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-450-450-450
Dimensions900900900
Spacing900900900
CellA=B=C: 900.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z900900900
origin x/y/z0.0000.0000.000
length x/y/z900.000900.000900.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-450-450-450
NC/NR/NS900900900
D min/max/mean-0.0800.0590.000

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Supplemental data

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Sample components

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Entire : Major vault protein [Rattus norvegicus]

EntireName: Major vault protein [Rattus norvegicus]
Components
  • Organelle or cellular component: Major vault protein [Rattus norvegicus]
    • Protein or peptide: Major vault protein

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Supramolecule #1: Major vault protein [Rattus norvegicus]

SupramoleculeName: Major vault protein [Rattus norvegicus] / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Major vault protein

MacromoleculeName: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 103.931305 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hl8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9669
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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