1HXR - 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)

Title :   CRYSTAL STRUCTURE OF MSS4 AT 1.65 ANGSTROMS

Authors :   Z. Zhu, J. J. Dumas, S. E. Lietzke, D. G. Lambright

Date :   16 Jan 01 (Deposition) - 14 Feb 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Nucleotide Exchange Factor, Rab Gtpase, Membrane Trafficking, Zn Binding Site, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhu, J. J. Dumas, S. E. Lietzke, D. G. Lambright
A Helical Turn Motif In Mss4 Is A Critical Determinant Of Rab Binding And Nucleotide Release.
Biochemistry V. 40 3027 2001
PubMed-ID: 11258916 | Reference-DOI: 10.1021/BI002680O
(for further references see the PDB file header)

Molecule 1 - GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:23 , CYS A:26 , CYS A:94 , CYS A:97	BINDING SITE FOR RESIDUE ZN A 200
2	AC2	SOFTWARE	CYS B:23 , CYS B:26 , CYS B:94 , CYS B:97	BINDING SITE FOR RESIDUE ZN B 201

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

Asymmetric Unit

No.	Residues
1	Gly A:100	-	Pro A:101
2	Gly B:100	-	Pro B:101

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MSS4	PS51796	MSS4 domain profile.	MSS4_RAT	9-123	2	A:9-123 B:9-123

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MSS4	PS51796	MSS4 domain profile.	MSS4_RAT	9-123	1	A:9-123 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MSS4	PS51796	MSS4 domain profile.	MSS4_RAT	9-123	1	- B:9-123

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000005845	1	ENSRNOE00000041665	chr13:47437328-47437477	150	MSS4_RAT	1-42	42	2	A:9-42 B:9-42	34 34
1.2	ENSRNOT00000005845	2	ENSRNOE00000041709	chr13:47447183-47448826	1644	MSS4_RAT	43-123	81	2	A:43-123 (gaps) B:43-123	81 81

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:107
 aligned with MSS4_RAT | Q08326 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:115
                                    18        28        38        48        58        68        78        88        98       108       118     
             MSS4_RAT     9 ELVSAEGRNRKAVLCQRCGSRVLQPGTALFSRRQLFLPSMRKKPDLVDGSNPDGDVLEEHWLVNDMFIFENVGFTKDVGNVKFLVCADCEIGPIGWHCLDDKNSFYVALERVSHE 123
               SCOP domains d1hxra_ A: RabGEF Mss4                                                                                              SCOP domains
               CATH domains 1hxrA00 A:9-123 Metal Binding Protein, Guani        ne Nucleotide Exchange Factor; Chain A                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eee.....eee...eeee......--------.eeee..eeee.hhhhh...ee......eeeee.........eeee......eeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MSS4  PDB: A:9-123 UniProt: 9-123                                                                                   PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-42 [INCOMPLETE]Exon 1.2  PDB: A:43-123 (gaps) UniProt: 43-123                                    Transcript 1
                 1hxr A   9 ELVSAEGRNRKAVLCQRCGSRVLQPGTALFSRRQLFLPSMRKKP--------DGDVLEEHWLVNDMFIFENVGFTKDVGNVKFLVCADCEIGPIGWHCLDDKNSFYVALERVSHE 123
                                    18        28        38        48   |     -  |     68        78        88        98       108       118     
                                                                      52       61

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with MSS4_RAT | Q08326 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:115
                                    18        28        38        48        58        68        78        88        98       108       118     
             MSS4_RAT     9 ELVSAEGRNRKAVLCQRCGSRVLQPGTALFSRRQLFLPSMRKKPDLVDGSNPDGDVLEEHWLVNDMFIFENVGFTKDVGNVKFLVCADCEIGPIGWHCLDDKNSFYVALERVSHE 123
               SCOP domains d1hxrb_ B: RabGEF Mss4                                                                                              SCOP domains
               CATH domains 1hxrB00 B:9-123 Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eee.....eee...eeee..ee.hhhh......eeee..eeee.hhhhh...ee......eeeee.....ee..eeee......eeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MSS4  PDB: B:9-123 UniProt: 9-123                                                                                   PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-42 [INCOMPLETE]Exon 1.2  PDB: B:43-123 UniProt: 43-123                                           Transcript 1
                 1hxr B   9 ELVSAEGRNRKAVLCQRCGSRVLQPGTALFSRRQLFLPSMRKKPDLVDGSNPDGDVLEEHWLVNDMFIFENVGFTKDVGNVKFLVCADCEIGPIGWHCLDDKNSFYVALERVSHE 123
                                    18        28        38        48        58        68        78        88        98       108       118

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Mss4-like (27)

Superfamily: Mss4-like (17)

Family: RabGEF Mss4 (3)

Protein domain: RabGEF Mss4 (3)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1hxra_	A:
1b	d1hxrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A (12)

Homologous Superfamily: Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A (9)

Norway rat (Rattus norvegicus) (1)

1a	1hxrB00	B:9-123
1b	1hxrA00	A:9-123

(no "Pfam Domain" information available for 1HXR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MSS4_RAT | Q08326)

molecular function
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Gly A:100 - Pro A:101	[ RasMol ]
		Gly B:100 - Pro B:101	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 ](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
	1hxr
		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
	MSS4_RAT \| Q08326
		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
	MSS4_RAT \| Q08326
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1HXR)

1fwq	1FWQ IS AN NMR MODEL OF MSS4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (2, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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