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- PDB-4v60: The structure of rat liver vault at 3.5 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4v60
TitleThe structure of rat liver vault at 3.5 angstrom resolution
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / 9 REPEAT DOMAINS / PROTEIN-PROTEIN COMPLEX / Ribonucleoprotein
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cytoskeleton / cell population proliferation / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm ...protein activation cascade / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cytoskeleton / cell population proliferation / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKato, K. / Zhou, Y. / Tanaka, H. / Yao, M. / Yamashita, E. / Yoshimura, M. / Tsukihara, T.
Citation
Journal: Science / Year: 2009
Title: The structure of rat liver vault at 3.5 angstrom resolution.
Authors: Hideaki Tanaka / Koji Kato / Eiki Yamashita / Tomoyuki Sumizawa / Yong Zhou / Min Yao / Kenji Iwasaki / Masato Yoshimura / Tomitake Tsukihara /
Abstract: Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the ...Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: A vault ribonucleoprotein particle exhibiting 39-fold dihedral symmetry
Authors: Kato, K. / Tanaka, H. / Sumizawa, T. / Yoshimura, M. / Yamashita, E. / Iwasaki, K. / Tsukihara, T.
History
DepositionOct 24, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2ZUO, 2ZV4, 2ZV5
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)3,740,88439
Polymers3,740,88439
Non-polymers00
Water00
1
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

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


Theoretical massNumber of molelcules
Total (without water)7,481,76978
Polymers7,481,76978
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)702.246, 383.796, 598.480
Angle α, β, γ (deg.)90.00, 124.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ...
Major vault protein / MVP


Mass: 95920.109 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: liver / References: UniProt: Q62667

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 39

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Sample preparation

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.4% PEG 4000, 0.8M sodium chloride, 0.05M lithium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 24, 2007 / Details: undulator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→204 Å / Num. obs: 1531361 / % possible obs: 92.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.233 / Rsym value: 0.209 / Net I/σ(I): 5.7
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.01076 / Mean I/σ(I) obs: 1.2 / Num. unique all: 403666 / Rsym value: 0.93 / % possible all: 81.2

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Processing

Software
NameClassification
MOSFLMdata reduction
DMmodel building
CNSrefinement
RAVEmodel building
SCALAdata scaling
DMphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cryo-EM map

Resolution: 3.5→204 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3304 75370 -RANDOM
Rwork0.311 ---
all-1630860 --
obs-1511765 92.7 %-
Displacement parametersBiso mean: 122.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.12 Å
Refinement stepCycle: LAST / Resolution: 3.5→204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms80652 0 0 0 80652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.479
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d26.417
X-RAY DIFFRACTIONc_improper_angle_d3.245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
3.5-3.630.431966400.425912656578
3.63-3.770.396167530.385612960980
3.77-3.940.368174160.354514031186
3.94-4.150.334876010.314314609790
4.15-4.410.312577380.288814787191
4.41-4.750.306379180.272114828791
4.75-5.230.314378160.281214848291
5.23-5.980.324878530.295214856891
5.98-7.540.283477070.250514865090
7.54-2040.333779280.328515195592

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