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- PDB-5d2m: Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 -

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Basic information

Entry
Database: PDB / ID: 5d2m
TitleComplex between human SUMO2-RANGAP1, UBC9 and ZNF451
Components
  • Ran GTPase-activating protein 1
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 2
  • Zinc finger protein 451
KeywordsLigase / Protein Binding / Complex / SUMO / E3 Ligase
Function / homology
Function and homology information


: / cellular response to vasopressin / negative regulation of transcription initiation by RNA polymerase II / 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 activity / SUMO ligase complex / SUMOylation of nuclear envelope proteins ...: / cellular response to vasopressin / negative regulation of transcription initiation by RNA polymerase II / 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 activity / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / nuclear pore cytoplasmic filaments / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / activation of GTPase activity / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / aggresome / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / nucleocytoplasmic transport / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / response to axon injury / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / chromosome segregation / RHO GTPases Activate Formins / transcription coregulator binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / PML body / mitotic spindle / kinetochore / protein tag activity / small GTPase binding / Formation of Incision Complex in GG-NER / Separation of Sister Chromatids / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / regulation of gene expression / nuclear membrane / positive regulation of cell migration / cadherin binding / cell division / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ZNF451, PIN-like domain / PIN like domain / 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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...ZNF451, PIN-like domain / PIN like domain / 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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Leucine Rich repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2-type / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Alpha Horseshoe / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / Small ubiquitin-related modifier 2 / SUMO-conjugating enzyme UBC9 / E3 SUMO-protein ligase ZNF451
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCappadocia, L. / Lima, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065872 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase.
Authors: Cappadocia, L. / Pichler, A. / Lima, C.D.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1
D: SUMO-conjugating enzyme UBC9
E: Small ubiquitin-related modifier 2
F: Ran GTPase-activating protein 1
G: Zinc finger protein 451
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,00012
Polymers99,6907
Non-polymers3105
Water12,647702
1
A: SUMO-conjugating enzyme UBC9
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1
E: Small ubiquitin-related modifier 2
G: Zinc finger protein 451
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9618
Polymers62,7755
Non-polymers1863
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: SUMO-conjugating enzyme UBC9
F: Ran GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0394
Polymers36,9152
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.240, 115.060, 130.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that although a heptameric complex that encompasses all chains present in the asymmetric unit was detected by size exclusion chromatography, structural and biochemical analyses suggest that the biological unit consists of a RANGAP1-SUMO2/UBC9/SUMO2/ZNF451 complex composed of chains A, B, C, E and G.

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Components

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Protein , 4 types, 7 molecules ADBECFG

#1: Protein SUMO-conjugating enzyme UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin- ...SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 18341.107 Da / Num. of mol.: 2 / Mutation: K14R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 9476.639 Da / Num. of mol.: 2 / Fragment: UNP residues 15-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61956
#3: Protein Ran GTPase-activating protein 1 / RanGAP1


Mass: 18573.451 Da / Num. of mol.: 2 / Fragment: UNP residues 418-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1, KIAA1835, SD / Plasmid: pSmt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P46060
#4: Protein Zinc finger protein 451 / / Coactivator for steroid receptors


Mass: 6907.192 Da / Num. of mol.: 1 / Fragment: UNP residues 2-56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF451, COASTER, KIAA0576, KIAA1702 / Plasmid: pLou3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y4E5

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Non-polymers , 2 types, 707 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→46.35 Å / Num. obs: 46766 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.94
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.5143 / Mean I/σ(I) obs: 3.83 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UIO

3uio


Resolution: 2.4→46.349 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1554 3.32 %Random selection
Rwork0.1947 ---
obs0.196 46759 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6365 0 20 702 7087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036594
X-RAY DIFFRACTIONf_angle_d0.7438923
X-RAY DIFFRACTIONf_dihedral_angle_d12.1862526
X-RAY DIFFRACTIONf_chiral_restr0.029987
X-RAY DIFFRACTIONf_plane_restr0.0031161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.28021350.25313890X-RAY DIFFRACTION96
2.4775-2.56610.29421390.23664078X-RAY DIFFRACTION100
2.5661-2.66880.27871410.22054070X-RAY DIFFRACTION100
2.6688-2.79020.2521400.21154091X-RAY DIFFRACTION100
2.7902-2.93730.25641400.20244083X-RAY DIFFRACTION100
2.9373-3.12130.25081410.20344101X-RAY DIFFRACTION100
3.1213-3.36220.21591400.19374103X-RAY DIFFRACTION100
3.3622-3.70050.19581420.1744115X-RAY DIFFRACTION100
3.7005-4.23560.23731430.16764154X-RAY DIFFRACTION100
4.2356-5.33520.19521430.15644178X-RAY DIFFRACTION100
5.3352-46.35760.1941500.18034342X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35950.0768-0.09960.54020.19521.0876-0.0408-0.09170.17630.03780.0373-0.1277-0.29520.235-0.00920.088-0.37020.10190.09650.0910.0978-8.50536.941210.9547
20.6948-0.3192-0.2270.15090.05150.277-0.02780.15150.1426-0.10660.01250.2617-0.1158-0.26810.00150.48720.2193-0.0210.55850.05540.4595-32.970213.714613.9639
30.87330.2161-0.25560.3573-0.15210.7670.026-0.24510.00530.2182-0.1565-0.218-0.01310.36710.03520.0532-0.43180.14380.18030.4028-0.02076.422810.9323-20.2206
40.68090.0776-0.170.5906-0.13451.24380.0307-0.0851-0.16010.1258-0.12940.01240.2471-0.190.01670.1885-0.11850.05560.0509-0.12870.1686-31.847-22.378817.8587
51.10970.13980.39090.5319-0.0580.94410.0063-0.0519-0.07390.05350.0172-0.12270.05340.172-0.03490.1704-0.0503-0.0130.1843-0.01560.18-13.7343-7.174732.7257
60.5983-0.1433-0.09460.6760.36451.09660.06820.2599-0.1156-0.0466-0.1440.13630.0268-0.09750.01990.1067-0.00540.0250.1881-0.09940.201-25.3614-27.1408-15.9448
71.1261-0.8111-0.61790.58270.44480.33870.00450.29490.5683-0.2064-0.09610.06-0.2981-0.22030.09650.39970.07620.04270.4162-0.0070.3804-36.016815.274525.6413
82.55260.5258-1.05321.69960.74781.0187-0.0092-0.2084-0.11370.19740.068-0.080.0656-0.0695-0.04230.1003-0.06790.0150.0796-0.01260.0901-22.3303-2.863538.6439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 157 )
2X-RAY DIFFRACTION2chain 'B' and (resid 18 through 93 )
3X-RAY DIFFRACTION3chain 'C' and (resid 430 through 587 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 157 )
5X-RAY DIFFRACTION5chain 'E' and (resid 14 through 93 )
6X-RAY DIFFRACTION6chain 'F' and (resid 431 through 587 )
7X-RAY DIFFRACTION7chain 'G' and (resid 30 through 39 )
8X-RAY DIFFRACTION8chain 'G' and (resid 40 through 50 )

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