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- PDB-4hl8: Re-refinement of the vault ribonucleoprotein particle -

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Basic information

Entry
Database: PDB / ID: 4hl8
TitleRe-refinement of the vault ribonucleoprotein particle
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / 9 repeat domains / protein-protein complex / ribonucleoprotein / cytoplasmic
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCasanas, A. / Querol-Audi, J. / Guerra, P. / Pous, J. / Tanaka, H. / Tsukihara, T. / Verdaguer, V. / Fita, I.
CitationJournal: Science / Year: 2009
Title: The structure of rat liver vault at 3.5 angstrom resolution.
Authors: Tanaka, H. / Kato, K. / Yamashita, E. / Sumizawa, T. / Zhou, Y. / Yao, M. / Iwasaki, K. / Yoshimura, M. / Tsukihara, T.
History
DepositionOct 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 0THIS ENTRY 4HL8 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2ZUOSF DETERMINED ...THIS ENTRY 4HL8 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R2ZUOSF DETERMINED BY AUTHORS OF THE PDB ENTRY 2ZUO: H. TANAKA, K. KATO, E. YAMASHITA, T. SUMIZAWA, Y. ZHOU, M. YAO, K. IWASAKI, M. YOSHIMURA, T. TSUKIHARA
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 2ZUO.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major vault protein


Theoretical massNumber of molelcules
Total (without water)95,9201
Polymers95,9201
Non-polymers00
Water0
1
A: Major vault protein
x 39


Theoretical massNumber of molelcules
Total (without water)3,740,88439
Polymers3,740,88439
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation38
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Major vault protein
x 39


  • crystal asymmetric unit, crystal frame
  • 3.74 MDa, 39 polymers
Theoretical massNumber of molelcules
Total (without water)3,740,88439
Polymers3,740,88439
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation38
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
SymmetryPoint symmetry: (Schoenflies symbol: C39 (39 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.988542, 0.150889, 0.004134), (-0.150891, 0.98705, 0.054443), (0.004134, -0.054442, 0.998508)
3generate(0.954464, 0.297871, 0.01643), (-0.297874, 0.948536, 0.107475), (0.01643, -0.107474, 0.994072)
4generate(0.89865, 0.437137, 0.036568), (-0.437142, 0.885456, 0.157724), (0.036568, -0.157722, 0.986806)
5generate(0.822544, 0.565082, 0.064027), (-0.565088, 0.799443, 0.203888), (0.064027, -0.203886, 0.976898)
6generate(0.728118, 0.678392, 0.098097), (-0.678399, 0.692724, 0.244772), (0.098097, -0.244769, 0.964606)
7generate(0.617818, 0.774132, 0.137894), (-0.77414, 0.568065, 0.279316), (0.137894, -0.279312, 0.950247)
8generate(0.4945, 0.849822, 0.182388), (-0.849831, 0.428693, 0.306625), (0.182388, -0.306622, 0.934193)
9generate(0.361357, 0.903502, 0.230427), (-0.903512, 0.278217, 0.325994), (0.230427, -0.32599, 0.91686)
10generate(0.221839, 0.933782, 0.280766), (-0.933792, 0.120537, 0.336919), (0.280766, -0.336915, 0.898697)
11generate(0.079559, 0.939877, 0.332102), (-0.939887, -0.040266, 0.339118), (0.332102, -0.339115, 0.880175)
12generate(-0.061799, 0.92163, 0.383105), (-0.92164, -0.200026, 0.332535), (0.383105, -0.332531, 0.861773)
13generate(-0.198572, 0.879514, 0.432454), (-0.879523, -0.354605, 0.317339), (0.432454, -0.317335, 0.843967)
14generate(-0.32722, 0.814618, 0.478871), (-0.814627, -0.5, 0.293924), (0.478871, -0.29392, 0.82722)
15generate(-0.444409, 0.728624, 0.521154), (-0.728632, -0.632445, 0.262896), (0.521154, -0.262893, 0.811964)
16generate(-0.547105, 0.62376, 0.558207), (-0.623766, -0.748511, 0.22506), (0.558207, -0.225057, 0.798595)
17generate(-0.632649, 0.50274, 0.589072), (-0.502745, -0.84519, 0.181394), (0.589072, -0.181392, 0.787458)
18generate(-0.698823, 0.368699, 0.612948), (-0.368703, -0.919979, 0.133031), (0.612948, -0.13303, 0.778844)
19generate(-0.743915, 0.22511, 0.629218), (-0.225112, -0.970942, 0.081222), (0.629218, -0.081221, 0.772973)
20generate(-0.766757, 0.07569, 0.637459), (-0.075691, -0.996757, 0.02731), (0.637459, -0.02731, 0.77)
21generate(-0.766757, -0.07569, 0.637459), (0.075691, -0.996757, -0.02731), (0.637459, 0.02731, 0.77)
22generate(-0.743915, -0.22511, 0.629218), (0.225112, -0.970942, -0.081222), (0.629218, 0.081221, 0.772973)
23generate(-0.698823, -0.368699, 0.612948), (0.368703, -0.919979, -0.133031), (0.612948, 0.13303, 0.778844)
24generate(-0.632649, -0.50274, 0.589072), (0.502745, -0.84519, -0.181394), (0.589072, 0.181392, 0.787458)
25generate(-0.547105, -0.62376, 0.558207), (0.623767, -0.748511, -0.22506), (0.558207, 0.225057, 0.798595)
26generate(-0.444409, -0.728624, 0.521154), (0.728632, -0.632445, -0.262896), (0.521154, 0.262893, 0.811964)
27generate(-0.32722, -0.814618, 0.478871), (0.814627, -0.5, -0.293924), (0.478871, 0.29392, 0.82722)
28generate(-0.198572, -0.879514, 0.432454), (0.879523, -0.354605, -0.317339), (0.432454, 0.317335, 0.843967)
29generate(-0.061798, -0.92163, 0.383105), (0.92164, -0.200026, -0.332535), (0.383105, 0.332531, 0.861773)
30generate(0.079559, -0.939877, 0.332102), (0.939887, -0.040266, -0.339118), (0.332102, 0.339115, 0.880175)
31generate(0.221839, -0.933782, 0.280766), (0.933792, 0.120537, -0.336919), (0.280766, 0.336915, 0.898697)
32generate(0.361357, -0.903502, 0.230427), (0.903512, 0.278217, -0.325994), (0.230427, 0.32599, 0.91686)
33generate(0.4945, -0.849822, 0.182388), (0.849831, 0.428693, -0.306625), (0.182388, 0.306622, 0.934193)
34generate(0.617818, -0.774131, 0.137894), (0.77414, 0.568065, -0.279315), (0.137894, 0.279312, 0.950247)
35generate(0.728118, -0.678392, 0.098097), (0.678399, 0.692724, -0.244772), (0.098097, 0.244769, 0.964606)
36generate(0.822544, -0.565082, 0.064027), (0.565088, 0.799443, -0.203888), (0.064027, 0.203886, 0.976898)
37generate(0.89865, -0.437137, 0.036568), (0.437142, 0.885456, -0.157724), (0.036568, 0.157722, 0.986806)
38generate(0.954464, -0.29787, 0.01643), (0.297874, 0.948537, -0.107475), (0.01643, 0.107474, 0.994072)
39generate(0.988542, -0.150889, 0.004134), (0.150891, 0.98705, -0.054443), (0.004134, 0.054442, 0.998508)

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Components

#1: Protein Major vault protein / / MVP


Mass: 95920.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q62667

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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
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. all: 1630860 / Num. obs: 1531361 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.2 / Rmerge(I) obs: 0.233 / Rsym value: 0.209 / Net I/σ(I): 5.7
Reflection shellResolution: 3.5→3.69 Å / Mean I/σ(I) obs: 1.2 / Rsym value: 0.93 / % possible all: 81.2

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→200 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.354 6961 RANDOM
Rwork0.352 --
all0.352 1531361 -
obs0.352 1531361 -
Refinement stepCycle: LAST / Resolution: 3.5→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 0 0 0 6157
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.007
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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