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- PDB-1kps: Structural Basis for E2-mediated SUMO conjugation revealed by a c... -

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Basic information

Entry
Database: PDB / ID: 1kps
TitleStructural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1
Components
  • Ran-GTPase activating protein 1
  • Ubiquitin-like protein SUMO-1 conjugating enzyme
KeywordsLIGASE/PROTEIN TRANSPORT / SUMO / UBIQUITIN / E2 / CONJUGATING ENZYME / LIGASE / THIOESTER / SMALL UBIQUITIN-LIKE MODIFIER / LIGASE-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of DNA replication proteins / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO conjugating enzyme activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RING-like zinc finger domain binding / SUMO ligase complex / Mitotic Prometaphase ...SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of DNA replication proteins / cellular response to vasopressin / cytoplasmic periphery of the nuclear pore complex / SUMO conjugating enzyme activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RING-like zinc finger domain binding / SUMO ligase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / RHO GTPases Activate Formins / Separation of Sister Chromatids / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / nuclear pore cytoplasmic filaments / mitotic nuclear membrane reassembly / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / negative regulation of protein export from nucleus / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / aggresome / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / postsynaptic cytosol / nuclear pore / response to axon injury / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / axon cytoplasm / Transcriptional and post-translational regulation of MITF-M expression and activity / GTPase activator activity / SUMOylation of transcription cofactors / Meiotic synapsis / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / PML body / modulation of chemical synaptic transmission / PKR-mediated signaling / protein modification process / kinetochore / small GTPase binding / Schaffer collateral - CA1 synapse / Formation of Incision Complex in GG-NER / mitotic spindle / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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 / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Leucine Rich repeat ...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 / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Leucine Rich repeat / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3 wavelength MAD dataset collected at NSLS beamline X4A to 2.8A / Resolution: 2.5 Å
AuthorsBernier-Villamor, V. / Sampson, D.A. / Matunis, M.J. / Lima, C.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1.
Authors: Bernier-Villamor, V. / Sampson, D.A. / Matunis, M.J. / Lima, C.D.
History
DepositionJan 2, 2002Deposition 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 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SUMO-1 conjugating enzyme
B: Ran-GTPase activating protein 1
C: Ubiquitin-like protein SUMO-1 conjugating enzyme
D: Ran-GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8518
Polymers73,4674
Non-polymers3844
Water10,539585
1
A: Ubiquitin-like protein SUMO-1 conjugating enzyme
B: Ran-GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9264
Polymers36,7342
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-like protein SUMO-1 conjugating enzyme
D: Ran-GTPase activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9264
Polymers36,7342
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.531, 126.509, 72.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ubiquitin-like protein SUMO-1 conjugating enzyme / UBC9 / SUMO-1-protein ligase / Ubiquitin carrier protein


Mass: 18117.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC9 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYS / References: UniProt: P63279, ubiquitin-protein ligase
#2: Protein Ran-GTPase activating protein 1 / RANGAP1


Mass: 18615.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RANGAP1 / Plasmid: MODIFIED PET28B-PSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODON PLUS RIL / References: UniProt: P46061
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
2100 mM1dropNaCl
350 mMTris-HCl1droppH8.0
41 mMBME1drop
51.0 Mlithium sulfate1reservoir
60.5 Mammonium sulfate1reservoir
750 mMsodium citrate1reservoirpH5.5
85 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9790, 0.9793, 0.9788, 0.9712
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.97881
40.97121
ReflectionResolution: 2.5→19.25 Å / Num. all: 27248 / Num. obs: 27248 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2
Reflection shellResolution: 2.5→2.66 Å / Num. unique all: 4114
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 27902 / % possible obs: 96.2 % / Num. measured all: 274090 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS0.9refinement
RESOLVEphasing
RefinementMethod to determine structure: 3 wavelength MAD dataset collected at NSLS beamline X4A to 2.8A
Resolution: 2.5→19.25 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3260494.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1343 4.9 %RANDOM
Rwork0.223 ---
obs0.223 27248 96.6 %-
all-27248 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.475 Å2 / ksol: 0.311999 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.61 Å20 Å20 Å2
2---11.18 Å20 Å2
3---1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 20 585 5537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 205 4.7 %
Rwork0.357 4114 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.357

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