2WT8 - 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)

Title :   STRUCTURE OF THE N-TERMINAL BRCT DOMAIN OF HUMAN MICROCEPHALIN (MCPH1)

Authors :   M. W. Richards, S. M. Roe, R. Bayliss

Date :   14 Sep 09 (Deposition) - 01 Dec 09 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Cell Cycle, Chromosome Condensation, Dwarfism, Polymorphism, Microcephaly, Phosphoprotein, Mental Retardation, Primary Microcephaly (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Richards, J. W. C. Leung, S. M. Roe, J. Chen, R. Bayliss
A Pocket On The Surface Of The N-Terminal Brct Domain Of Mcph1 Is Required To Prevent Abnormal Chromosome Condensation.
J. Mol. Biol. V. 395 908 2010
PubMed-ID: 19925808 | Reference-DOI: 10.1016/J.JMB.2009.11.029

Molecule 1 - MICROCEPHALIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Variant	:	CODONPLUS RPIL
	Fragment	:	N-TERMINAL BRCT DOMAIN, RESIDUES 1-95
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , SER A:18 , LYS A:53 , ASP B:87 , HOH B:2122	BINDING SITE FOR RESIDUE ACT A1096
2	AC2	SOFTWARE	ASP A:87 , HOH A:2130 , SER B:17 , SER B:18 , LYS B:53	BINDING SITE FOR RESIDUE CL A1097
3	AC3	SOFTWARE	HOH C:2078	BINDING SITE FOR RESIDUE ACT C1096

(no "SS Bond" information available for 2WT8)

(no "Cis Peptide Bond" information available for 2WT8)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046745	T	27	R	MCPH1_HUMAN	Disease (MCPH1)	---	A/B/C/D	T	27	R

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046745	T	27	R	MCPH1_HUMAN	Disease (MCPH1)	---	A	T	27	R

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046745	T	27	R	MCPH1_HUMAN	Disease (MCPH1)	---	B	T	27	R

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046745	T	27	R	MCPH1_HUMAN	Disease (MCPH1)	---	C	T	27	R

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_046745	T	27	R	MCPH1_HUMAN	Disease (MCPH1)	---	D	T	27	R

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MCPH1_HUMAN	1-93 672-730 751-833	2	A:1-93 B:1-93 - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MCPH1_HUMAN	1-93 672-730 751-833	1	A:1-93 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MCPH1_HUMAN	1-93 672-730 751-833	1	- B:1-93 - -

Biological Unit 3 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MCPH1_HUMAN	1-93 672-730 751-833	0	- - - -

Biological Unit 4 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRCT	PS50172	BRCT domain profile.	MCPH1_HUMAN	1-93 672-730 751-833	0	- - - -

(no "Exon" information available for 2WT8)

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:97
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:97
                              1                                                                                              
                              |      8        18        28        38        48        58        68        78        88       
           MCPH1_HUMAN    - --MAAPILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee........hhhhhhhhhhhh..ee.........eeeee..hhhhhhhhhhh..eeehhhhhhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------R-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --BRCT  PDB: A:1-93 UniProt: 1-93                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  2wt8 A -1 GAmAAPILKDVVAYVEVWSSNGTENYSKTFTTQLVDmGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
                              |      8        18        28      | 38        48        58        68        78        88       
                              |                                35-MSE                                                        
                              1-MSE

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:96
                             1                                                                                              
                             |       9        19        29        39        49        59        69        79        89      
           MCPH1_HUMAN    - -MAAPILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee........hhhhhhhhhhhh..ee.........eeeee..hhhhhhhhhhh..eeehhhhhhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------R-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -BRCT  PDB: B:1-93 UniProt: 1-93                                                              -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  2wt8 B  0 AmAAPILKDVVAYVEVWSSNGTENYSKTFTTQLVDmGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
                             |       9        19        29     |  39        49        59        69        79        89      
                             1-MSE                            35-MSE

Chain C from PDB  Type:PROTEIN  Length:92
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
           MCPH1_HUMAN    4 PILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee........hhhhhhhhhhhh..ee.........eeeee..hhhhhhhhhhh..eeehhhhhhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------R-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BRCT  PDB: - UniProt: 1-93                                                                -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2wt8 C  4 PILKDVVAYVEVWSSNGTENYSKTFTTQLVDmGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
                                    13        23        33 |      43        53        63        73        83        93  
                                                          35-MSE

Chain D from PDB  Type:PROTEIN  Length:92
 aligned with MCPH1_HUMAN | Q8NEM0 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
           MCPH1_HUMAN    4 PILKDVVAYVEVWSSNGTENYSKTFTTQLVDMGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PTCB-BRCT-2wt8D01 D:9-75                                           -------------------- Pfam domains (1)
           Pfam domains (2) -----PTCB-BRCT-2wt8D02 D:9-75                                           -------------------- Pfam domains (2)
           Pfam domains (3) -----PTCB-BRCT-2wt8D03 D:9-75                                           -------------------- Pfam domains (3)
           Pfam domains (4) -----PTCB-BRCT-2wt8D04 D:9-75                                           -------------------- Pfam domains (4)
         Sec.struct. author ......eeeeee........hhhhhhhhhhh...eee........eeeee..hhhhhhhhhhh..eeehhhhhhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------R-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BRCT  PDB: - UniProt: 1-93                                                                -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  2wt8 D  4 PILKDVVAYVEVWSSNGTENYSKTFTTQLVDmGAKVSKTFNKQVTHVIFKDGYQSTWDKAQKRGVKLVSVLWVEKCRTAGAHIDESLFPAAN 95
                                    13        23        33 |      43        53        63        73        83        93  
                                                          35-MSE

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 '\|'

(no "SCOP Domain" information available for 2WT8)

(no "CATH Domain" information available for 2WT8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: BRCT-like (38)

Family: PTCB-BRCT (3)

Homo sapiens (Human) (3)

1a	PTCB-BRCT-2wt8D01	D:9-75
1b	PTCB-BRCT-2wt8D02	D:9-75
1c	PTCB-BRCT-2wt8D03	D:9-75
1d	PTCB-BRCT-2wt8D04	D:9-75

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MCPH1_HUMAN | Q8NEM0)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0021987	cerebral cortex development	The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
	GO:0071850	mitotic cell cycle arrest	The process in which the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, M).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wt8)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 ](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
	2wt8
		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
	MCPH1_HUMAN \| Q8NEM0
		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)
	251200
		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
	MCPH1_HUMAN \| Q8NEM0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MCPH1_HUMAN \| Q8NEM0	:	3ktf 3pa6 3sht 3shv 3szm 3t1n 3u3z

(no "Related Entries Specified in the PDB File" available for 2WT8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (8, 8)

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