[English] 日本語
Yorodumi
- EMDB-7126: Recombinant major vault protein [Rattus norvegicus] structure in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7126
TitleRecombinant major vault protein [Rattus norvegicus] structure in solution: conformation 1
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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bp8
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bp8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7126.png

Downloads & links

-
Map

FileDownload / File: emd_7126.map.gz / Format: CCP4 / Size: 1.9 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 800 pix.
= 800. Å		1 Å/pix.
x 800 pix.
= 800. Å		1 Å/pix.
x 800 pix.
= 800. 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: 0.0139 / Movie #1: 0.0139
Minimum - Maximum-0.035749298 - 0.041839883
Average (Standard dev.)-0.0007795452 (±0.002158929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 800.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z800.000800.000800.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-0.0360.042-0.001

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more