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- PDB-3ran: CANINE GDP-RAN Q69L MUTANT -

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Basic information

Entry
Database: PDB / ID: 3ran
TitleCANINE GDP-RAN Q69L MUTANT
ComponentsPROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
KeywordsTRANSPORT PROTEIN / GTPASE / NUCLEAR TRANSPORT
Function / homology
Function and homology information


RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / RISC complex / GTP metabolic process / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus ...RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / RISC complex / GTP metabolic process / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus / positive regulation of protein export from nucleus / protein import into nucleus / melanosome / nuclear envelope / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
small GTPase Ran family profile. / Ran GTPase / 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...small GTPase Ran family profile. / Ran GTPase / 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsStewart, M. / Kent, H.M. / Mccoy, A.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2).
Authors: Stewart, M. / Kent, H.M. / McCoy, A.J.
History
DepositionOct 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
B: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
C: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
D: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,63512
Polymers97,7654
Non-polymers1,8708
Water3,783210
1
A: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9093
Polymers24,4411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9093
Polymers24,4411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9093
Polymers24,4411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9093
Polymers24,4411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.090, 59.170, 116.370
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99461, -0.10357, 0.00455), (0.10351, 0.98973, -0.09857), (0.0057, 0.09851, 0.99512)10.27816, 13.10003, -56.30025
2given(-0.12468, 0.1117, 0.98589), (-0.13047, -0.98686, 0.09531), (0.98358, -0.11675, 0.13762)-38.01392, 26.03238, 30.14345
3given(-0.13794, 0.0068, 0.99042), (0.0033, -0.99997, 0.00732), (0.99043, 0.00428, 0.13791)-93.14473, 25.60413, 29.0372

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Components

#1: Protein
PROTEIN (GTP-BINDING NUCLEAR PROTEIN RAN) / TC4


Mass: 24441.135 Da / Num. of mol.: 4 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Details: Q69L MUTANT CONSTRUCTED BY PROTEIN ENGINEERING / Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris
Description: CDNA OBTAINED BY SITE-SPECIFIC MUTAGENESIS OF WILD-TYPE CANINE RAN CDNA AS DESCRIBED IN PUBLICATION
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62825
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growpH: 7.2 / Details: SEE PUBLICATION, pH 7.2
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
235 %PEG10001reservoir
320 mM1reservoirMgCl2
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0378
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 29, 1998 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0378 Å / Relative weight: 1
ReflectionResolution: 2.3→32.3 Å / Num. obs: 35632 / % possible obs: 94.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4.9 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 76123
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EBI-1279

Resolution: 2.15→6 Å / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.23
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -5 %RANDOM
Rwork0.176 ---
obs-22660 94.7 %-
Displacement parametersBiso mean: 32.95 Å2
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6503 0 116 210 6829
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.017
X-RAY DIFFRACTIONp_angle_d0.030.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
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
Highest resolution: 2.3 Å / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
X-RAY DIFFRACTIONp_planar_d

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