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- PDB-2rpq: Solution Structure of a SUMO-interacting motif of MBD1-containing... -

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Basic information

Entry
Database: PDB / ID: 2rpq
TitleSolution Structure of a SUMO-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3
Components
  • Activating transcription factor 7-interacting protein 1
  • Small ubiquitin-related modifier 2
KeywordsTRANSCRIPTION / SUMO / SIM / Nucleus / Ubl conjugation pathway / Activator / Host-virus interaction / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation / ubiquitin-like protein ligase binding / SUMOylation of transcription factors ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / hippocampal mossy fiber to CA3 synapse / Regulation of endogenous retroelements by KRAB-ZFP proteins / GABA-ergic synapse / transcription coregulator activity / SUMOylation of intracellular receptors / PML body / PKMTs methylate histone lysines / Formation of Incision Complex in GG-NER / protein tag activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / transcription regulator complex / nuclear body / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Activating transcription factor 7-interacting protein / ATF7-interacting protein , protein binding domain / ATF-interacting protein binding domain / Fibronectin-III type domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Activating transcription factor 7-interacting protein / ATF7-interacting protein , protein binding domain / ATF-interacting protein binding domain / Fibronectin-III type domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2 / Activating transcription factor 7-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSekiyama, N. / Ikegami, T. / Yamane, T. / Ikeguchi, M. / Uchimura, Y. / Baba, D. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3
Authors: Sekiyama, N. / Ikegami, T. / Yamane, T. / Ikeguchi, M. / Uchimura, Y. / Baba, D. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
History
DepositionJul 7, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 2
B: Activating transcription factor 7-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)15,5402
Polymers15,5402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Small ubiquitin-related modifier 2 / SUMO-2 / Ubiquitin-like protein SMT3B / SMT3 homolog 2 / Sentrin-2 / HSMT3 / SUMO-3


Mass: 10623.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61956
#2: Protein/peptide Activating transcription factor 7-interacting protein 1 / ATFa-associated modulator / hAM / ATF-interacting protein / ATF-IP / MBD1-containing chromatin- ...ATFa-associated modulator / hAM / ATF-interacting protein / ATF-IP / MBD1-containing chromatin-associated factor 1 / P621


Mass: 4916.150 Da / Num. of mol.: 1 / Fragment: UNP residues 938-981 / Source method: obtained synthetically / Details: This entity is chemically synthesized. / References: UniProt: Q6VMQ6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D HCACO

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Sample preparation

DetailsContents: 0.7 mM [U-100% 13C; U-100% 15N] SIMMCAF1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.7 mM / Component: SIMMCAF1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
MARBLEIkeguchi, M.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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