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- PDB-4l6e: Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ... -

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Basic information

Entry
Database: PDB / ID: 4l6e
TitleCrystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics Consortium (NESG) Target HR9193b
ComponentsE3 SUMO-protein ligase RanBP2
KeywordsLIGASE / ISOMERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / NESG / RanBP2 / RanBD1 / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / protein sumoylation / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / SUMOylation of chromatin organization proteins / GTPase activator activity / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Signaling by ALK fusions and activated point mutants / ISG15 antiviral mechanism / small GTPase binding / HCMV Early Events / Separation of Sister Chromatids / protein folding / nuclear envelope / snRNP Assembly / nuclear membrane / intracellular membrane-bounded organelle / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / metal ion binding / cytosol / cytoplasm
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 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...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 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase RanBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.496 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Maglaqui, M. / Kogan, S. / Wang, H. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Maglaqui, M. / Kogan, S. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Maglaqui, M. / Kogan, S. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-protein ligase RanBP2


Theoretical massNumber of molelcules
Total (without water)18,7081
Polymers18,7081
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.481, 69.481, 152.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-3101-

HOH

21A-3102-

HOH

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Components

#1: 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 / Putative peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18708.486 Da / Num. of mol.: 1 / Fragment: RanBD1 4 domain (UNP residues 2907-3050)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP358, RANBP2 / Plasmid: HR9193B-2907-3050-15.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 7
Details: 12% PEG 3350, 0.1M sodium acetate, pH 7.00, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97924 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14342 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 69.21 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 0.98 / Num. unique all: 1645 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.496→32.212 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.79 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 656 4.6 %RANDOM
Rwork0.197 ---
obs0.198 14259 99.5 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.205 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 183.91 Å2 / Biso mean: 79.441 Å2 / Biso min: 46.25 Å2
Baniso -1Baniso -2Baniso -3
1-6.991 Å20 Å20 Å2
2--6.991 Å20 Å2
3----13.982 Å2
Refinement stepCycle: LAST / Resolution: 2.496→32.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 37 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011054
X-RAY DIFFRACTIONf_angle_d1.1821415
X-RAY DIFFRACTIONf_chiral_restr0.08151
X-RAY DIFFRACTIONf_plane_restr0.004179
X-RAY DIFFRACTIONf_dihedral_angle_d15.913402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.496-2.6890.3841430.32327252868100
2.689-2.9590.3261160.28527152831100
2.959-3.3870.2721190.23627542873100
3.387-4.2660.1841240.1832718284299
4.266-32.2150.1981540.1652691284599
Refinement TLS params.Method: refined / Origin x: 15.9328 Å / Origin y: 19.9245 Å / Origin z: 74.7614 Å
111213212223313233
T0.5428 Å20.0261 Å20.0425 Å2-0.5568 Å20.0132 Å2--0.5299 Å2
L3.3531 °2-0.0572 °2-1.1558 °2-2.7499 °2-0.0227 °2--3.3176 °2
S-0.1624 Å °-0.0488 Å °-0.0195 Å °0.0909 Å °0.1125 Å °0.1239 Å °-0.041 Å °0.0267 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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