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- PDB-2grp: Crystal Structure of human RanGAP1-Ubc9-Y87A -

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Basic information

Entry
Database: PDB / ID: 2grp
TitleCrystal Structure of human RanGAP1-Ubc9-Y87A
Components
  • Ran GTPase-activating protein 1
  • Ubiquitin-conjugating enzyme E2 I
KeywordsLIGASE / ubiquitin / conjugation / small ubiquitin like modifer / smt3
Function / homology
Function and homology information


cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / nuclear pore cytoplasmic filaments / small protein activating enzyme binding / synaptonemal complex / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / activation of GTPase activity / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / nuclear export / SUMOylation of RNA binding proteins / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / aggresome / Maturation of nucleoprotein / nucleocytoplasmic transport / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / response to axon injury / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / GTPase activator activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / transcription coregulator binding / chromosome segregation / RHO GTPases Activate Formins / SUMOylation of intracellular receptors / PKR-mediated signaling / protein modification process / PML body / mitotic spindle / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / Separation of Sister Chromatids / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of cell migration / cadherin binding / cell division / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / dendrite / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Leucine rich repeat, ribonuclease inhibitor type / : / Leucine Rich repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Leucine rich repeat, ribonuclease inhibitor type / : / Leucine Rich repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsYunus, A.A. / Lima, C.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
Authors: Yunus, A.A. / Lima, C.D.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 I
B: Ran GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)36,6802
Polymers36,6802
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.429, 45.092, 60.871
Angle α, β, γ (deg.)71.080, 71.110, 75.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO-1- ...Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO-1-conjugating enzyme / Ubiquitin carrier protein 9 / p18


Mass: 18220.994 Da / Num. of mol.: 1 / Mutation: Y87A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 CODON PLUS RIL / References: UniProt: P63279, ubiquitin-protein ligase
#2: Protein Ran GTPase-activating protein 1


Mass: 18459.348 Da / Num. of mol.: 1 / Fragment: C-terminal domain (RESIDUES 419-587)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1 / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 CODON PLUS RIL / References: UniProt: P46060
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2003
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 22558 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Χ2: 1.347 / Net I/σ(I): 16.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.166 / Num. unique all: 2098 / Χ2: 1.17 / % possible all: 89.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.8 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.848 / Data cutoff high absF: 737144.438 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1120 5 %RANDOM
Rwork0.191 ---
all-23190 --
obs-22332 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.453 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-1.95 Å2-3.36 Å2
2---1.05 Å2-1.47 Å2
3---2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-6 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 0 299 2764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.05→2.12 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 80 3.9 %
Rwork0.236 1993 -
obs-2073 90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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