1M6U - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A NOVEL DNA-BINDING DOMAIN FROM NDT80, A TRANSCRIPTIONAL ACTIVATOR REQUIRED FOR MEIOSIS IN YEAST

Authors :   S. P. Montano, M. L. Cote, I. Fingerman, M. Pierce, A. K. Vershon, M. M. Georgiadis

Date :   17 Jul 02 (Deposition) - 06 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (2x),B (2x)
Biol. Unit 4: A (1x),B (1x)
Biol. Unit 5: A  (2x)

Keywords :   Transcription Activator, Yeast Protein, Dna-Binding, Meiosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. P. Montano, M. L. Cote, I. Fingerman, M. Pierce, A. K. Vershon, M. M. Georgiadis
Crystal Structure Of The Dna-Binding Domain From Ndt80, A Transcriptional Activator Required For Meiosis In Yeast
Proc. Natl. Acad. Sci. Usa V. 99 14041 2002
PubMed-ID: 12384578 | Reference-DOI: 10.1073/PNAS.222312199
(for further references see the PDB file header)

Molecule 1 - NDT80 PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 CODON+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN, RESIDUES 59-330
	Gene	:	NDT80
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A (2x)	B (2x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)
Biological Unit 5 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:97 , GLY A:98 , ASN A:112 , ARG A:202 , HOH A:746 , HOH A:768 , HOH A:769	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	HIS A:101 , ILE A:102 , ASP A:103 , GLU A:104	BINDING SITE FOR RESIDUE SO4 A 500
3	AC3	SOFTWARE	SER A:259 , LYS A:265 , PRO A:266 , PHE A:267 , GLN A:268 , HOH A:729 , ARG B:85	BINDING SITE FOR RESIDUE SO4 B 600
4	AC4	SOFTWARE	ALA A:204 , VAL A:207 , ARG A:208 , ASN A:209 , ILE A:210 , THR A:211 , ARG A:251	BINDING SITE FOR RESIDUE SO4 A 700

(no "SS Bond" information available for 1M6U)

Asymmetric Unit

No.	Residues
1	Lys A:265	-	Pro A:266

(no "SAP(SNP)/Variant" information available for 1M6U)

(no "PROSITE Motif" information available for 1M6U)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YHR124W	1	YHR124W.1	VIII:356564-358447	1884	NDT80_YEAST	1-627	627	2	A:63-327 B:65-323 (gaps)	265 259

Asymmetric Unit

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:265
 aligned with NDT80_YEAST | P38830 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:265
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          NDT80_YEAST    63 FKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLIIRGRS 327
               SCOP domains d1m6ua_ A: DNA-binding domain from NDT80                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1m6uA00 A:63-327 p53-like transcription factors                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...............eeeeeeee..eee..eeeee....eeeeeeee....hhhhhhhh.eeeeee....eeeee..eeeeeeeeee.....eeeeee...............ee.......hhhhhhhhhhh.hhhhh..hhhhheee.hhhhhhhh...hhhhhh...eee..eeeeeeeee.............eeeeeeeeeeeehhhhh........eeeee.....eeeeeeeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:63-327 UniProt: 1-627 [INCOMPLETE]                                                                                                                                                                                                                       Transcript 1
                 1m6u A  63 FKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKTKKYDSTFYLHRNHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPFQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLIIRGRS 327
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with NDT80_YEAST | P38830 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:259
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314         
          NDT80_YEAST    65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLII 323
               SCOP domains d1m6ub_ B: DNA-binding domain from NDT80                                                                                                                                                                                                                            SCOP domains
               CATH domains 1m6uB00 B:65-323 p53-like transcription factors                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------NDT80_PhoG-1m6uB01 B:105-323                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ----------------------------------------NDT80_PhoG-1m6uB02 B:105-323                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .....eeeee...eee.........eeeeeeee..ee....ee......eeeeeeee....hhhhhhhh.eeeeee....eeeeeeeeeeeeeeeee........eee...............ee.......hhhhhhhhh...hhhhh..hhhhheee.hhhhhhhh...hhhhhh...eee..eeeeeeee....---------.eeeeeeeeeeee.............eeee.......eeeeeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:65-323 (gaps) UniProt: 1-627 [INCOMPLETE]                                                                                                                                                                                                          Transcript 1
                 1m6u B  65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKTKKYDSTFYLHRNHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSI---------KHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLII 323
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      |  -      |274       284       294       304       314         
                                                                                                                                                                                                                              261       271

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: p53-like transcription factors (14)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1m6uA00	A:63-327
1b	1m6uB00	B:65-323

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P53-like (54)

Family: NDT80_PhoG (4)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	NDT80_PhoG-1m6uB01	B:105-323
1b	NDT80_PhoG-1m6uB02	B:105-323

Asymmetric Unit(hide GO term definitions)

Chain A,B (NDT80_YEAST | P38830)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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.
cellular component
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	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.

Asymmetric Unit
	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
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:265 - Pro A:266	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]
		Biological Unit 5	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format \| Biol. Unit 5 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
	1m6u
		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
	NDT80_YEAST \| P38830
		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
	NDT80_YEAST \| P38830
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NDT80_YEAST \| P38830	:	1m7u 1mn4 1mnn 2etw 2euv 2euw 2eux 2euz 2evf 2evg 2evh 2evi 2evj

1m7u	THE CRYSTAL STRUCTURE OF A NOVEL DNA-BINDING DOMAIN FROM NDT80, A TRANSCRIPTIONAL ACTIVATOR REQUIRED FOR MEIOSIS IN YEAST, P 31 2 1 SPACE GROUP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

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