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- PDB-3msv: The hypoxic regulator of sterol synthesis Nro1 is a nuclear impor... -

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Basic information

Entry
Database: PDB / ID: 3msv
TitleThe hypoxic regulator of sterol synthesis Nro1 is a nuclear import adaptor
ComponentsNuclear import adaptor, Nro1
KeywordsPROTEIN BINDING / helix repeats / HEAT repeats
Function / homology
Function and homology information


positive regulation of SREBP signaling pathway / cation binding / SREBP signaling pathway / enzyme inhibitor activity / regulation of translation / cellular response to hypoxia / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Negative regulator of Ofd1/Enhancer of translation termination 1 / : / Nuclear pore complex subunit Nro1 / Negative regulator of ofd1, C-terminal
Similarity search - Domain/homology
Negative regulator of ofd1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.18 Å
AuthorsYeh, T.L. / Amzel, L.M. / Bianchet, M.A.
CitationJournal: Structure / Year: 2011
Title: The hypoxic regulator of sterol synthesis nro1 is a nuclear import adaptor.
Authors: Yeh, T.L. / Lee, C.Y. / Amzel, L.M. / Espenshade, P.J. / Bianchet, M.A.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear import adaptor, Nro1
B: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)88,9732
Polymers88,9732
Non-polymers00
Water7,116395
1
A: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)44,4861
Polymers44,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear import adaptor, Nro1


Theoretical massNumber of molelcules
Total (without water)44,4861
Polymers44,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-4 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.790, 107.960, 100.780
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclear import adaptor, Nro1


Mass: 44486.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC4B3.07 / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9USJ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3 M ammonium tartrate dibasic, 0.1 M Bis-TrisHCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
SYNCHROTRONAPS 31-ID20.979
Detector
TypeIDDetectorDate
RIGAKU SATURN 9441CCDOct 20, 2008
RAYONIX MX225HE2CCDFeb 15, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9791
ReflectionResolution: 2.18→19.73 Å / Num. all: 51980 / Num. obs: 51200 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 12.9
Reflection shellResolution: 2.18→2.3 Å / Rmerge(I) obs: 0.515 / % possible all: 93.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
SOLVEphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.18→19.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.602 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25701 2576 5 %RANDOM
Rwork0.20452 ---
obs0.2072 48602 98.61 %-
all-51200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-0.31 Å2
2---0.56 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.18→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 0 395 6025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9687816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6865699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93725.695295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.297151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1221525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214375
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6851.53509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33325662
X-RAY DIFFRACTIONr_scbond_it1.95232241
X-RAY DIFFRACTIONr_scangle_it3.244.52152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.181→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 174 -
Rwork0.285 3112 -
obs--86.66 %

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