4JKH - 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 :   OPEN AND CLOSED FORMS OF D1781E HUMAN PRP8 RNASE H-LIKE DOMAIN WITH BOUND MG ION

Authors :   M. J. Schellenberg, T. Wu, D. B. Ritchie, K. A. Atta, A. M. Macmillan

Date :   09 Mar 13 (Deposition) - 22 May 13 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Metalloprotein, Conformational Change, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Schellenberg, T. Wu, D. B. Ritchie, S. Fica, J. P. Staley, K. A. Atta, P. Lapointe, A. M. Macmillan
A Conformational Switch In Prp8 Mediates Metal Ion Coordination That Promotes Pre-Mrna Exon Ligation.
Nat. Struct. Mol. Biol. V. 20 728 2013
PubMed-ID: 23686287 | Reference-DOI: 10.1038/NSMB.2556

Molecule 1 - PRE-MRNA-PROCESSING-SPLICING FACTOR 8
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALC2-E
	Expression System Strain	:	BL21 (DE3) ROSETTA2
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PRP8 RNASE H-LIKE DOMAIN, UNP RESIDUES 1769-1990'
	Gene	:	PRP8, PRPC8, PRPF8
	Mutation	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	220 KDA U5 SNRNP-SPECIFIC PROTEIN, PRP8 HOMOLOG, SPLICING FACTOR PRP8, P220

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:1890 , ARG A:1941 , HIS A:1944 , HOH A:2324	BINDING SITE FOR RESIDUE CL A 2001
2	AC2	SOFTWARE	GLY A:1867	BINDING SITE FOR RESIDUE CL A 2002
3	AC3	SOFTWARE	GLU A:1781 , THR A:1864 , ARG A:1865 , LEU A:1889 , GLN A:1890 , LEU A:1891 , GLN A:1894	BINDING SITE FOR RESIDUE GOL A 2003
4	AC4	SOFTWARE	GLU A:1911 , PRO A:1912 , HOH A:2193 , HOH A:2275 , HOH A:2312 , LYS B:1908 , GLN B:1913	BINDING SITE FOR RESIDUE GOL A 2004
5	AC5	SOFTWARE	GLU B:1781 , HOH B:2195 , HOH B:2239 , HOH B:2240 , HOH B:2241 , HOH B:2242	BINDING SITE FOR RESIDUE MG B 2001
6	AC6	SOFTWARE	HOH A:2254 , HOH A:2343 , GLU B:1856 , HOH B:2212 , HOH B:2322	BINDING SITE FOR RESIDUE MG B 2002
7	AC7	SOFTWARE	GLN B:1830 , LYS B:1838 , HOH B:2230 , HOH B:2282	BINDING SITE FOR RESIDUE CL B 2003
8	AC8	SOFTWARE	LYS A:1792 , ILE A:1977 , THR B:1789	BINDING SITE FOR RESIDUE CL B 2004

(no "SS Bond" information available for 4JKH)

(no "Cis Peptide Bond" information available for 4JKH)

(no "SAP(SNP)/Variant" information available for 4JKH)

(no "PROSITE Motif" information available for 4JKH)

(no "Exon" information available for 4JKH)

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:221
                                                                                                                                                                                                                                                              
               SCOP domains d4jkha_ A: Pre-mRNA-splicing factor 8, Prp8                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeee.....eeeeee.eeeeee.....eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jkh A 1770 ELFSNQIIWFVEDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILAD 1990
                                  1779      1789      1799      1809      1819      1829      1839      1849      1859      1869      1879      1889      1899      1909      1919      1929      1939      1949      1959      1969      1979      1989

Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d4jkhb_ B: Pre-mRNA-splicing factor 8, Prp8                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee....................eeeeee.....eeeeeee...hhhhh......hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jkh B 1770 ELFSNQIIWFVEDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILAD 1990
                                  1779      1789      1799      1809      1819      1829      1839      1849      1859      1869      1879      1889      1899      1909      1919      1929      1939      1949      1959      1969      1979      1989

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: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: Prp8 beta-finger domain-like (20)

Protein domain: Pre-mRNA-splicing factor 8, Prp8 (19)

Human (Homo sapiens) [TaxId: 9606] (13)

1a	d4jkha_	A:
1b	d4jkhb_	B:

(no "CATH Domain" information available for 4JKH)

(no "Pfam Domain" information available for 4JKH)

Asymmetric Unit(hide GO term definitions)

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jkh)

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
	4jkh
		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
	PRP8_HUMAN \| Q6P2Q9
		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
	PRP8_HUMAN \| Q6P2Q9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (26, 26)

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