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- PDB-1a2k: GDPRAN-NTF2 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a2k
TitleGDPRAN-NTF2 COMPLEX
Components
  • NUCLEAR TRANSPORT FACTOR 2
  • RAN
KeywordsTRANSPORT/NUCLEAR PROTEIN / COMPLEX (TRANSPORT-NUCLEAR PROTEIN) / GTP-BINDING / TRANSPORT-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of vascular endothelial growth factor production / RISC complex binding / pre-miRNA binding / nuclear pore central transport channel / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / nucleocytoplasmic transport / structural constituent of nuclear pore ...protein localization to nuclear pore / negative regulation of vascular endothelial growth factor production / RISC complex binding / pre-miRNA binding / nuclear pore central transport channel / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / nucleocytoplasmic transport / structural constituent of nuclear pore / RISC complex / GTP metabolic process / protein export from nucleus / nuclear outer membrane / ribosomal subunit export from nucleus / nuclear inner membrane / nuclear import signal receptor activity / mitotic sister chromatid segregation / mRNA transport / positive regulation of protein export from nucleus / protein import into nucleus / positive regulation of protein import into nucleus / small GTPase binding / nuclear envelope / melanosome / nuclear membrane / GTPase activity / cell division / GTP binding / magnesium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear transport factor 2 domain profile. / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / small GTPase Ran family profile. / Ran GTPase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Nuclear Transport Factor 2; Chain: A, ...Nuclear transport factor 2 domain profile. / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / small GTPase Ran family profile. / Ran GTPase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Nuclear Transport Factor 2; Chain: A, / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Nuclear transport factor 2 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStewart, M. / Kent, H.M. / Mccoy, A.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran.
Authors: Stewart, M. / Kent, H.M. / McCoy, A.J.
History
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR TRANSPORT FACTOR 2
B: NUCLEAR TRANSPORT FACTOR 2
C: RAN
D: RAN
E: RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,85012
Polymers102,3515
Non-polymers1,4997
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NUCLEAR TRANSPORT FACTOR 2
B: NUCLEAR TRANSPORT FACTOR 2
C: RAN
D: RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8308
Polymers77,8954
Non-polymers9354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-82 kcal/mol
Surface area27860 Å2
MethodPISA
3
E: RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0204
Polymers24,4561
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)155.150, 120.540, 108.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6556, 0.4598, 0.5989), (0.4693, -0.8695, 0.1539), (0.5915, 0.1802, -0.7859)
Vector: -44.79, -13.18, 134.89999)

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Components

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Protein , 2 types, 5 molecules ABCDE

#1: Protein NUCLEAR TRANSPORT FACTOR 2 / NTF2 / P10 / PP15


Mass: 14491.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61972
#2: Protein RAN / GSP1P / TC4


Mass: 24456.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Cell line: BL21 / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62825

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Non-polymers , 4 types, 155 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growMethod: vapor diffusion / pH: 5.6
Details: COMPLEX CRYSTALLIZED BY VAPOR DIFFUSION FROM 0.1M LI2SO4, 50 MM NA CITRATE PH5.6, 15% PEG4000., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
20.1 M1reservoirLi2SO4
350 mMsodium citrate1reservoirpH5.6
415 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 17, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→33.923 Å / Num. obs: 35633 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 191098

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUN FOR NTF2 COORDINATES FROM A.WITTINGHOFER AND K.SCHEFFZEK
Resolution: 2.5→7 Å / Details: RMSD BOND ANGLES: 2.0 DEGREES
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1783 5 %RANDOM
Rwork0.215 ---
obs-35669 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 92 170 7289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_deg / Dev ideal: 2

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