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- PDB-1k5g: Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex -

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Basic information

Entry
Database: PDB / ID: 1k5g
TitleCrystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex
Components
  • GTP-binding nuclear protein RAN
  • Ran GTPase activating protein 1
  • Ran-specific GTPase-activating protein
KeywordsSIGNALING PROTEIN/SIGNALING ACTIVATOR / RAN / RANBP1 / RANGAP / GAP / SIGNAL TRANSDUCTION / NUCLEAR TRANSPORT / GTP HYDROLYSIS / ACTIVATION STATE / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) / SIGNALING PROTEIN-SIGNALING ACTIVATOR COMPLEX
Function / homology
Function and homology information


SUMOylation of nuclear envelope proteins / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...SUMOylation of nuclear envelope proteins / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / GDP-dissociation inhibitor activity / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / sperm flagellum / nuclear pore / protein export from nucleus / centriole / viral process / nuclear periphery / GTPase activator activity / mitotic spindle organization / G protein activity / positive regulation of protein export from nucleus / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / centrosome / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ran-specific GTPase-activating protein 1, Ran-binding domain / Leucine rich repeat, ribonuclease inhibitor type / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase ...: / Ran-specific GTPase-activating protein 1, Ran-binding domain / Leucine rich repeat, ribonuclease inhibitor type / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ran GTPase-activating protein 1 / Ran-specific GTPase-activating protein / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSeewald, M.J. / Koerner, C. / Wittinghofer, A. / Vetter, I.R.
Citation
Journal: Nature / Year: 2002
Title: RanGAP mediates GTP hydrolysis without an arginine finger.
Authors: Seewald, M.J. / Korner, C. / Wittinghofer, A. / Vetter, I.R.
#1: Journal: Science / Year: 1997
Title: THE RAS-RASGAP COMPLEX: STRUCTURAL BASIS FOR GTPASE ACTIVATION AND ITS LOSS IN ONCOGENIC RAS MUTANTS
Authors: Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A.
#2: Journal: Nature / Year: 1999
Title: STRUCTURE OF A RAN-BINDING DOMAIN COMPLEXED WITH RAN BOUND TO A GTP ANALOGUE: IMPLICATIONS FOR NUCLEAR TRANSPORT
Authors: Vetter, I.R. / Nowak, C. / Nishimoto, T. / Kuhlmann, J. / Wittinghofer, A.
#3: Journal: Mol.Cell / Year: 1999
Title: THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN
Authors: Hillig, R.C. / Renault, L. / Vetter, I.R. / Drell, T. / Wittinghofer, A. / Becker, J.
#4: Journal: J.Biol.Chem. / Year: 1995
Title: RNA1 ENCODES A GTPASE-ACTIVATING PROTEIN SPECIFIC FOR GSP1P, THE RAN/TC4 HOMOLOGUE OF SACCHAROMYCES CEREVISIAE
Authors: Becker, J. / Melchior, F. / Gerke, V. / Bischoff, F.R. / Ponstingl, H. / Wittinghofer, A.
#5: Journal: J.Biol.Chem. / Year: 1997
Title: THE ACIDIC C-TERMINAL DOMAIN OF RNA1P IS REQUIRED FOR THE BINDING OF RAN.GTP AND FOR RANGAP ACTIVITY
Authors: Haberland, J. / Becker, J. / Gerke, V.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.classification / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein RAN
B: Ran-specific GTPase-activating protein
C: Ran GTPase activating protein 1
D: GTP-binding nuclear protein RAN
E: Ran-specific GTPase-activating protein
F: Ran GTPase activating protein 1
G: GTP-binding nuclear protein RAN
H: Ran-specific GTPase-activating protein
I: Ran GTPase activating protein 1
J: GTP-binding nuclear protein RAN
K: Ran-specific GTPase-activating protein
L: Ran GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,53024
Polymers364,32412
Non-polymers2,20612
Water0
1
A: GTP-binding nuclear protein RAN
B: Ran-specific GTPase-activating protein
C: Ran GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6326
Polymers91,0813
Non-polymers5513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-60 kcal/mol
Surface area28960 Å2
MethodPISA
2
D: GTP-binding nuclear protein RAN
E: Ran-specific GTPase-activating protein
F: Ran GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6326
Polymers91,0813
Non-polymers5513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-59 kcal/mol
Surface area28950 Å2
MethodPISA
3
G: GTP-binding nuclear protein RAN
H: Ran-specific GTPase-activating protein
I: Ran GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6326
Polymers91,0813
Non-polymers5513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-60 kcal/mol
Surface area28940 Å2
MethodPISA
4
J: GTP-binding nuclear protein RAN
K: Ran-specific GTPase-activating protein
L: Ran GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6326
Polymers91,0813
Non-polymers5513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-61 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.930, 102.568, 118.850
Angle α, β, γ (deg.)71.67, 79.09, 67.81
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5882, 0.1848, -0.7873), (0.1707, -0.9232, -0.3443), (-0.7905, -0.3368, 0.5115)27.5638, 31.0455, 21.5274
2given(-0.3394, -0.9315, 0.1312), (-0.9317, 0.3136, -0.1835), (0.1298, -0.1845, -0.9742)27.6427, 94.8585, 27.2934
3given(-0.0361, 0.7438, 0.6674), (0.7362, -0.4318, 0.5211), (0.6758, 0.5102, -0.532)4.1976, -60.1625, -20.6668

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
GTP-binding nuclear protein RAN / Ran / TC4 / Ran GTPase / Androgen receptor-associated protein 24


Mass: 24456.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62826
#2: Protein
Ran-specific GTPase-activating protein / RanBP1 / Ran binding protein 1


Mass: 23352.199 Da / Num. of mol.: 4 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43487
#3: Protein
Ran GTPase activating protein 1 / RanGAP / Protein rna1


Mass: 43272.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET3D / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P41391

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 mM1dropAl3+
230 mM1dropNaF
320 mMTris-HCl1droppH7.5
42 mM1dropMgCl2
52 mMDTE1drop
618.5-20.5 %PEG40001reservoir
7100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 92906 / Num. obs: 92906 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 107.6 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 3
Reflection shellResolution: 3.1→3.3 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 1.7 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 96 % / Num. measured all: 207495
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
ProDCdata collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5D

1k5d


Resolution: 3.1→31 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber (CNS 1.0)
Details: SOME OF THE RESIDUES HAVE WEAK DENSITY, PLEASE CHECK B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 7163 10 %RANDOM
Rwork0.25 ---
all0.252 72121 --
obs0.252 72121 96.2 %-
Solvent computationSolvent model: flat model / Bsol: 18.5846 Å2 / ksol: 0.27126 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å2-22.04 Å2-0.01 Å2
2--3.93 Å2-6.75 Å2
3----8.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 3.1→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22264 0 132 0 22396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it11.181.5
X-RAY DIFFRACTIONc_mcangle_it17.342
X-RAY DIFFRACTIONc_scbond_it15.232
X-RAY DIFFRACTIONc_scangle_it21.832.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 1148 9.7 %
Rwork0.4 10729 -
obs-10729 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3gdp.par
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5af3.par
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 63.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it11.181.5
X-RAY DIFFRACTIONc_scbond_it15.232
X-RAY DIFFRACTIONc_mcangle_it17.342
X-RAY DIFFRACTIONc_scangle_it21.832.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.415 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.4

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