2RPQ - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF A SUMO-INTERACTING MOTIF OF MBD1-CONTAINING CHROMATIN-ASSOCIATED FACTOR 1 BOUND TO SUMO-3

Authors :   N. Sekiyama, T. Ikegami, T. Yamane, M. Ikeguchi, Y. Uchimura, D. Baba, M. Ariyoshi, H. Tochio, H. Saitoh, M. Shirakawa

Date :   07 Jul 08 (Deposition) - 07 Oct 08 (Release) - 09 Dec 15 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Sumo, Sim, Nucleus, Ubl Conjugation Pathway, Activator, Host-Virus Interaction, Phosphoprotein, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sekiyama, T. Ikegami, T. Yamane, M. Ikeguchi, Y. Uchimura, D. Baba, M. Ariyoshi, H. Tochio, H. Saitoh, M. Shirakawa
Structure Of The Small Ubiquitin-Like Modifier (Sumo)-Interacting Motif Of Mbd1-Containing Chromatin-Associated Factor 1 Bound To Sumo-3
J. Biol. Chem. V. 283 35966 2008
PubMed-ID: 18842587 | Reference-DOI: 10.1074/JBC.M802528200

Molecule 1 - SMALL UBIQUITIN-RELATED MODIFIER 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-4T
	Expression System Vector Type	:	VECTOR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SUMO-2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, SENTRIN-2, HSMT3, SUMO-3

Molecule 2 - ACTIVATING TRANSCRIPTION FACTOR 7-INTERACTING PROTEIN 1
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 938-981
	Other Details	:	THIS ENTITY IS CHEMICALLY SYNTHESIZED.
	Synonym	:	ATFA-ASSOCIATED MODULATOR, HAM, ATF-INTERACTING PROTEIN, ATF-IP, MBD1-CONTAINING CHROMATIN-ASSOCIATED FACTOR 1, P621
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2RPQ)

(no "Site" information available for 2RPQ)

(no "SS Bond" information available for 2RPQ)

NMR Structure

No.	Model	Residues
1	2, 9	Met A:1	-	Ala A:2
2	7	Asp A:63	-	Gly A:64
3	15	Pro A:66	-	Ile A:67

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047508	D	16	N	SUMO2_HUMAN	Polymorphism	17850328	A	D	16	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure * (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047508	D	16	N	SUMO2_HUMAN	Polymorphism	17850328	A	D	16	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO2_HUMAN	16-93	1	A:16-93

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO2_HUMAN	16-93	1	A:16-93

(no "Exon" information available for 2RPQ)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:93
 aligned with SUMO2_HUMAN | P61956 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
          SUMO2_HUMAN     1 MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  93
               SCOP domains --------------d2rpqa1 A:15-93 SUMO-2                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------Rad60-SLD-2rpqA01 A:18-88                                              ----- Pfam domains
         Sec.struct. author ................eeeeeee.....eeeeeee...hhhhhhhhhhhhhh.....eeeee..eee.............eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------N----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------UBIQUITIN_2  PDB: A:16-93 UniProt: 16-93                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 2rpq A   1 MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  93
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with MCAF1_HUMAN | Q6VMQ6 from UniProtKB/Swiss-Prot  Length:1270

    Alignment length:11
                                   974 
          MCAF1_HUMAN   965 GVIDLTMDDEE 975
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 2rpq B 965 GVIDLTMDDEE 975
                                   974

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: SUMO-2 (8)

Human (Homo sapiens) [TaxId: 9606] (8)

d2rpqa1

A:15-93

(no "CATH Domain" information available for 2RPQ)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ubiquitin (279)

Family: Rad60-SLD (17)

Homo sapiens (Human) (16)

Rad60-SLD-2rpqA01

A:18-88

NMR Structure(hide GO term definitions)

Chain A (SUMO2_HUMAN | P61956)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B (MCAF1_HUMAN | Q6VMQ6)

molecular function
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
	GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045898	regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that modulates the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2rpq)

	Sites
(no "Sites" information available for 2rpq)

	Cis Peptide Bonds
		Asp A:63 - Gly A:64	[ RasMol ]
		Met A:1 - Ala A:2	[ RasMol ]
		Pro A:66 - Ile A:67	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2rpq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MCAF1_HUMAN \| Q6VMQ6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SUMO2_HUMAN \| P61956
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MCAF1_HUMAN \| Q6VMQ6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SUMO2_HUMAN \| P61956
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2RPQ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (21, 24)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File