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- PDB-11eq: RNA Vault with BAD bound (MVP/TEP1 sample) -

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Basic information

Entry
Database: PDB / ID: 11eq
TitleRNA Vault with BAD bound (MVP/TEP1 sample)
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / RNA Vault / BAD / benzamide adenine dinucleotide / Major Vault Protein
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / nuclear pore / mRNA transport / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton ...protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / nuclear pore / mRNA transport / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / intracellular signal transduction / ribonucleoprotein complex / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / cytoplasm / cytosol
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
Chem-DQV / Major vault protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsOsinski, A. / Tagliabracci, V.S.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1911 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158265 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 United States
CitationJournal: Biorxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault
Authors: Osinski, A. / Mayro, B. / Lopez, V.A. / Schrad, J. / Choi, H. / Tomchick, D.R. / Pawlowski, K. / Forsberg, K. / Shahmoradian, S.H. / Tagliabracci, V.S.
History
DepositionFeb 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major vault protein
B: Major vault protein
C: Major vault protein
D: Major vault protein
E: Major vault protein
F: Major vault protein
G: Major vault protein
H: Major vault protein
I: Major vault protein
J: Major vault protein
K: Major vault protein
L: Major vault protein
M: Major vault protein
N: Major vault protein
O: Major vault protein
P: Major vault protein
Q: Major vault protein
R: Major vault protein
S: Major vault protein
T: Major vault protein
U: Major vault protein
V: Major vault protein
W: Major vault protein
X: Major vault protein
Y: Major vault protein
Z: Major vault protein
a: Major vault protein
b: Major vault protein
c: Major vault protein
d: Major vault protein
e: Major vault protein
f: Major vault protein
g: Major vault protein
h: Major vault protein
i: Major vault protein
j: Major vault protein
k: Major vault protein
l: Major vault protein
m: Major vault protein
n: Major vault protein
o: Major vault protein
p: Major vault protein
q: Major vault protein
r: Major vault protein
s: Major vault protein
t: Major vault protein
u: Major vault protein
v: Major vault protein
w: Major vault protein
x: Major vault protein
y: Major vault protein
z: Major vault protein
1: Major vault protein
2: Major vault protein
3: Major vault protein
4: Major vault protein
5: Major vault protein
6: Major vault protein
7: Major vault protein
8: Major vault protein
9: Major vault protein
0: Major vault protein
AA: Major vault protein
AB: Major vault protein
AC: Major vault protein
AD: Major vault protein
AE: Major vault protein
AF: Major vault protein
AG: Major vault protein
AH: Major vault protein
AI: Major vault protein
AJ: Major vault protein
AK: Major vault protein
AL: Major vault protein
AM: Major vault protein
AN: Major vault protein
AO: Major vault protein
AP: Major vault protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,808,986156
Polymers7,757,31678
Non-polymers51,67078
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Major vault protein / MVP / Lung resistance-related protein


Mass: 99452.766 Da / Num. of mol.: 78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVP, LRP / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q14764
#2: Chemical...
ChemComp-DQV / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 662.437 Da / Num. of mol.: 78 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA Vault with BAD bound (MVP/TEP1 sample) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: 293F
Buffer solutionpH: 7.5
Details: 50 mM Tris 7.5 75 NaCl 1.5 mM MgCl2 1 mM DTT 1 mM BAD 1 mM AMP-PNP 0.025% DDM
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris1
275 mMSodium ChlorideNaCl1
31.5 mMMagnesium chlorideMgCl21
41 mMDithiothreitolDTT1
51 mMBenzamide adenine nucleotideBAD1
61 mMAdenosine-5'-[(ss,?)-imido]triphosphate Tetralithium Salt; Adenylyl-imidodiphosphateAMP-PNP1
70.025 %n-Dodecyl-Beta-D-maltosideDDM1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.21.2_5419model refinement
10ISOLDEmodel refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D39 (2x39 fold dihedral)
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20744 / Symmetry type: POINT
RefinementCross valid method: NONE

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