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- PDB-5clq: Ran Y39A in complex with GPPNHP and RanBD1 -

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Basic information

Entry
Database: PDB / ID: 5clq
TitleRan Y39A in complex with GPPNHP and RanBD1
Components
  • E3 SUMO-protein ligase RanBP2
  • GTP-binding nuclear protein Ran
KeywordsHYDROLASE / GTPase / nuclear transport / Ran binding protein
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / nuclear pore cytoplasmic filaments / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / Transferases; Acyltransferases; Aminoacyltransferases / kinase activator activity / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / centrosome localization / MicroRNA (miRNA) biogenesis / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / DNA metabolic process / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / dynein intermediate chain binding / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / ribosomal large subunit export from nucleus / spermatid development / Regulation of HSF1-mediated heat shock response / viral process / positive regulation of protein binding / mRNA transport / sperm flagellum / nuclear pore / SUMOylation of DNA damage response and repair proteins / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / protein export from nucleus / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / HCMV Late Events / mitotic spindle organization / male germ cell nucleus / hippocampus development / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / recycling endosome / positive regulation of protein import into nucleus / ISG15 antiviral mechanism / small GTPase binding / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / GDP binding / Signaling by ALK fusions and activated point mutants / nuclear envelope / melanosome / protein folding / mitotic cell cycle / G protein activity / actin cytoskeleton organization / snRNP Assembly / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding
Similarity search - Function
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVetter, I.R. / Brucker, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy.
Authors: Rudack, T. / Jenrich, S. / Brucker, S. / Vetter, I.R. / Gerwert, K. / Kotting, C.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31214
Polymers86,6434
Non-polymers1,66910
Water21612
1
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1567
Polymers43,3212
Non-polymers8355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-70 kcal/mol
Surface area17190 Å2
MethodPISA
2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1567
Polymers43,3212
Non-polymers8355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-73 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.530, 170.920, 135.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 24364.008 Da / Num. of mol.: 2 / Mutation: Y39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


Mass: 18957.402 Da / Num. of mol.: 2 / Fragment: Ran binding domain 1, UNP residues 1155-1321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 4 types, 22 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M ammonium sulfate, 2.5% PEG 1500, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0039 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2010
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 3.2→87.924 Å / Num. obs: 19912 / % possible obs: 99.4 % / Redundancy: 6.56 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.99
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.97 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rrp

1rrp


Resolution: 3.2→19.984 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 995 5 %
Rwork0.2235 --
obs0.2251 19894 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 96 12 5524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015637
X-RAY DIFFRACTIONf_angle_d2.0057633
X-RAY DIFFRACTIONf_dihedral_angle_d23.6383451
X-RAY DIFFRACTIONf_chiral_restr0.085824
X-RAY DIFFRACTIONf_plane_restr0.009967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.3680.33731420.29812656X-RAY DIFFRACTION100
3.368-3.57790.31681410.26752660X-RAY DIFFRACTION100
3.5779-3.85240.27381380.24912673X-RAY DIFFRACTION100
3.8524-4.23670.28341400.22842678X-RAY DIFFRACTION100
4.2367-4.84210.23491430.19882705X-RAY DIFFRACTION100
4.8421-6.0720.25691430.21572718X-RAY DIFFRACTION100
6.072-19.98390.21271480.2042809X-RAY DIFFRACTION100

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