4JK9 - JenaLib

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Title :   OPEN AND CLOSED FORMS OF WILD-TYPE HUMAN PRP8 RNASE H-LIKE DOMAIN WITH BOUND CO 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 :   1.50

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
	Organism Common	:	HUMAN
	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, 10)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	CO	6	Ligand/Ion	COBALT (II) ION
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:1922 , HIS A:1965 , HIS A:1966 , HOH A:2269 , HOH A:2356 , HOH A:2388	BINDING SITE FOR RESIDUE CO A 2001
02	AC2	SOFTWARE	GLU A:1843 , HOH A:2347 , HOH A:2351 , HOH A:2369 , HOH A:2383	BINDING SITE FOR RESIDUE CO A 2002
03	AC3	SOFTWARE	GLU A:1911 , PRO A:1912 , HOH A:2197 , HOH A:2256 , LEU B:1905 , LYS B:1908 , GLN B:1913	BINDING SITE FOR RESIDUE GOL A 2003
04	AC4	SOFTWARE	SER A:1929 , TYR A:1930 , HOH B:2181	BINDING SITE FOR RESIDUE CL A 2004
05	AC5	SOFTWARE	ASP B:1781 , HOH B:2153 , HOH B:2172 , HOH B:2279 , HOH B:2320	BINDING SITE FOR RESIDUE CO B 2001
06	AC6	SOFTWARE	GLU A:1856 , HOH A:2327 , HOH A:2363 , GLU B:1856 , HOH B:2240 , HOH B:2280 , HOH B:2319	BINDING SITE FOR RESIDUE CO B 2002
07	AC7	SOFTWARE	ASP B:1922 , HIS B:1965 , HIS B:1966 , HOH B:2283 , HOH B:2317 , HOH B:2330	BINDING SITE FOR RESIDUE CO B 2003
08	AC8	SOFTWARE	GLU A:1873 , HOH A:2121 , GLU B:1888 , HOH B:2226 , HOH B:2292	BINDING SITE FOR RESIDUE CO B 2004
09	AC9	SOFTWARE	THR B:1824 , ALA B:1837 , HOH B:2155	BINDING SITE FOR RESIDUE CL B 2005
10	BC1	SOFTWARE	SER B:1825 , LYS B:1840	BINDING SITE FOR RESIDUE CL B 2006

(no "SS Bond" information available for 4JK9)

(no "Cis Peptide Bond" information available for 4JK9)

(no "SAP(SNP)/Variant" information available for 4JK9)

(no "PROSITE Motif" information available for 4JK9)

(no "Exon" information available for 4JK9)

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:219
                                                                                                                                                                                                                                                            
               SCOP domains d4jk9a_ 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
                4jk9 A 1771 LFSQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILAD 1990
                              ||  1781      1791      1801      1811      1821      1831      1841      1851      1861      1871      1881      1891      1901      1911      1921      1931      1941      1951      1961      1971      1981         
                              ||                                                                                                                                                                                                                       
                           1773|                                                                                                                                                                                                                       
                            1775

Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains d4jk9b_ 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.hhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jk9 B 1770 ELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILA 1989
                                  1779      1789      1799      1809      1819      1829      1839      1849      1859      1869      1879      1889      1899      1909      1919      1929      1939      1949      1959      1969      1979      1989

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	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(

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Superfamilies( (-)

)

Families(

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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	d4jk9a_	A:
1b	d4jk9b_	B:

(no "CATH Domain" information available for 4JK9)

(no "Pfam Domain" information available for 4JK9)

Asymmetric Unit(hide GO term definitions)

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Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

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