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- PDB-1k5d: Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex -

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Basic information

Entry
Database: PDB / ID: 1k5d
TitleCrystal structure of Ran-GPPNHP-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 / GROUND 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 / small GTPase-mediated signal transduction / 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 / G protein activity / mitotic spindle organization / positive regulation of protein export from nucleus / male germ cell nucleus / hippocampus development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Transcriptional regulation by small RNAs / 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 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) ...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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 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: 2.7 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.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

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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)366,51020
Polymers364,32412
Non-polymers2,1868
Water6,161342
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)91,6275
Polymers91,0813
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-50 kcal/mol
Surface area29720 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)91,6275
Polymers91,0813
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-50 kcal/mol
Surface area29670 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)91,6275
Polymers91,0813
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-50 kcal/mol
Surface area29700 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)91,6275
Polymers91,0813
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-50 kcal/mol
Surface area29630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.551, 103.109, 120.177
Angle α, β, γ (deg.)71.59, 80.55, 67.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5586, 0.1655, -0.8128), (0.1693, -0.9365, -0.3071), (-0.812, -0.3091, 0.4951)27.3508, 30.7777, 21.1989
2given(-0.3575, -0.9204, 0.158), (-0.9204, 0.3187, -0.2264), (0.158, -0.2264, -0.9611)28.2636, 95.1906, 24.4013
3given(-0.0489, 0.7355, 0.6757), (0.7412, -0.4267, 0.5182), (0.6695, 0.5262, -0.5243)4.6115, -60.5007, -20.487

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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, 350 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, POTASSIUM ACETATE, 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-IDDetailsChemical formula
118.5-20.5 %PEG40001reservoir
2100 mMpotassium acetate1reservoir
3100 mMTris-HCl1reservoirpH7.5
420 mMTris-HCl1droppH7.5
52 mM1dropMgCl2
62 mMDTE1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000 / Details: MICROFOCUS BEAMLINE, 30 MICROMETER APERTURE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 163530 / Num. obs: 163530 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.6
Reflection shellResolution: 2.7→2.87 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 409414
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

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

1yrg


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.002 / 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
Rfree0.267 11396 10 %RANDOM
Rwork0.237 ---
all0.24 114796 --
obs0.24 114796 98 %-
Solvent computationSolvent model: flat model / Bsol: 44.7494 Å2 / ksol: 0.320174 e/Å3
Displacement parametersBiso mean: 61.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-11.57 Å2-4.78 Å2
2---2.6 Å2-5.98 Å2
3---3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22264 0 132 342 22738
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_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it7.811.5
X-RAY DIFFRACTIONc_mcangle_it12.12
X-RAY DIFFRACTIONc_scbond_it12.072
X-RAY DIFFRACTIONc_scangle_it17.212.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 1921 10 %
Rwork0.39 17282 -
obs-17282 97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3gnp.par
X-RAY DIFFRACTION4water_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.1 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_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it7.811.5
X-RAY DIFFRACTIONc_scbond_it12.072
X-RAY DIFFRACTIONc_mcangle_it12.12
X-RAY DIFFRACTIONc_scangle_it17.212.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / % reflection Rfree: 10 % / Rfactor Rwork: 0.39

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