1K5J - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF NUCLEOPLASMIN-CORE

Authors :   S. Dutta, I. V. Akey, C. Dingwall, K. L. Hartman, T. Laue, R. T. Nolte, J. F. Head, C. W. Akey

Date :   10 Oct 01 (Deposition) - 01 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Beta-Barrel, Jellyroll, Beta-Bulge, Pentamer, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dutta, I. V. Akey, C. Dingwall, K. L. Hartman, T. Laue, R. T. Nolte, J. F. Head, C. W. Akey
The Crystal Structure Of Nucleoplasmin-Core: Implications For Histone Binding And Nucleosome Assembly.
Mol. Cell V. 8 841 2001
PubMed-ID: 11684019 | Reference-DOI: 10.1016/S1097-2765(01)00354-9
(for further references see the PDB file header)

Molecule 1 - NUCLEOPLASMIN CORE
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRK172
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEOPLASMIN CORE
	Gene	:	NUCLEOPLASMIN
	Mutation	:	YES
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1K5J)

(no "Site" information available for 1K5J)

(no "SS Bond" information available for 1K5J)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:98	-	Pro A:99
2	Gly A:109	-	Pro A:110
3	Pro B:98	-	Pro B:99
4	Gly B:109	-	Pro B:110
5	Pro C:98	-	Pro C:99
6	Gly C:109	-	Pro C:110
7	Pro D:98	-	Pro D:99
8	Gly D:109	-	Pro D:110
9	Pro E:98	-	Pro E:99
10	Gly E:109	-	Pro E:110

(no "SAP(SNP)/Variant" information available for 1K5J)

(no "PROSITE Motif" information available for 1K5J)

(no "Exon" information available for 1K5J)

Asymmetric/Biological 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:94
 aligned with NUPL_XENLA | P05221 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:105
                                    24        34        44        54        64        74        84        94       104       114     
           NUPL_XENLA    15 VSLIWGCELNEQDKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFNIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
               SCOP domains d1k5ja_ A: Nucleopl        asmin core                                                                     SCOP domains
               CATH domains 1k5jA00 A:15-119  [        code=2.60.120.340, no name d   efined]                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeee.--------..eeeeeeeee........eeeeeee..---.eeeeeeee......eee....ee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1k5j A  15 VSLIWGCELNEQNKTFEFK--------EHQLALRTVCLGDKAKDEFHIVEIVTQE---EKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
                                    24        |-       |44        54        64    |   74        84        94       104       114     
                                             33       42                         69  73

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with NUPL_XENLA | P05221 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:104
                                    25        35        45        55        65        75        85        95       105       115    
           NUPL_XENLA    16 SLIWGCELNEQDKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFNIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
               SCOP domains d1k5jb_ B: Nucleop        lasmin core                                                                    SCOP domains
               CATH domains 1k5jB00 B:16-119          [code=2.60.120.340, no name defined]                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee.--------..eeeeeeeee........eeeeeeeee..eeeeeeeeee......eee....ee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1k5j B  16 SLIWGCELNEQNKTFEFK--------EHQLALRTVCLGDKAKDEFHIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
                                    25       | -      | 45        55        65        75        85        95       105       115    
                                            33       42

Chain C from PDB  Type:PROTEIN  Length:89
 aligned with NUPL_XENLA | P05221 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:103
                                    25        35        45        55        65        75        85        95       105       115   
           NUPL_XENLA    16 SLIWGCELNEQDKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFNIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHV 118
               SCOP domains d1k5jc_ C: Nucleop        lasmin core                                                                   SCOP domains
               CATH domains 1k5jC00 C:16-118          [code=2.60.120.340, no nam      e defined]                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee.--------...eeeeeeee........eeeeee.------..eeeeee......eee....ee...eeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1k5j C  16 SLIWGCELNEQNKTFEFK--------EHQLALRTVCLGDKAKDEFHIVEIVT------KSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHV 118
                                    25       | -      | 45        55        65 |      75        85        95       105       115   
                                            33       42                       67     74

Chain D from PDB  Type:PROTEIN  Length:90
 aligned with NUPL_XENLA | P05221 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:103
                                    25        35        45        55        65        75        85        95       105       115   
           NUPL_XENLA    16 SLIWGCELNEQDKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFNIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHV 118
               SCOP domains d1k5jd_ D: Nucleop        lasmin core                                                                   SCOP domains
               CATH domains 1k5jD00 D:16-118          [code=2.60.120.340, no nam     e defined]                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee.--------...eeeeeeee........eeeeee.-----..eeeeeee......eee....ee...eeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1k5j D  16 SLIWGCELNEQNKTFEFK--------EHQLALRTVCLGDKAKDEFHIVEIVT-----EKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHV 118
                                    25       | -      | 45        55        65 |     |75        85        95       105       115   
                                            33       42                       67    73

Chain E from PDB  Type:PROTEIN  Length:93
 aligned with NUPL_XENLA | P05221 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:105
                                    24        34        44        54        64        74        84        94       104       114     
           NUPL_XENLA    15 VSLIWGCELNEQDKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFNIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
               SCOP domains d1k5je_ E: Nucleopl        asmin core                                                                     SCOP domains
               CATH domains 1k5jE00 E:15-119  [        code=2.60.120.340, no name     defined]                                        CATH domains
           Pfam domains (1) Nucleoplasmin-1k5jE        01 E:15-119                                                                    Pfam domains (1)
           Pfam domains (2) Nucleoplasmin-1k5jE        02 E:15-119                                                                    Pfam domains (2)
           Pfam domains (3) Nucleoplasmin-1k5jE        03 E:15-119                                                                    Pfam domains (3)
           Pfam domains (4) Nucleoplasmin-1k5jE        04 E:15-119                                                                    Pfam domains (4)
           Pfam domains (5) Nucleoplasmin-1k5jE        05 E:15-119                                                                    Pfam domains (5)
         Sec.struct. author .eeeeeeee.....eeee.--------..eeeeeeeee........eeeeee..----..eeeeeee......eee....ee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1k5j E  15 VSLIWGCELNEQNKTFEFK--------EHQLALRTVCLGDKAKDEFHIVEIVTQ----EKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVA 119
                                    24        |-       |44        54        64   |    74        84        94       104       114     
                                             33       42                        68   73

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) (278)

Superfamily: Nucleoplasmin-like core domain (8)

Family: Nucleoplasmin-like core domain (7)

Protein domain: Nucleoplasmin core (1)

African clawed frog (Xenopus laevis) [TaxId: 8355] (1)

1a	d1k5ja_	A:
1b	d1k5jb_	B:
1c	d1k5jc_	C:
1d	d1k5jd_	D:
1e	d1k5je_	E:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.340, no name defined] (6)

African clawed frog (Xenopus laevis) (4)

1a	1k5jB00	B:16-119
1b	1k5jA00	A:15-119
1c	1k5jE00	E:15-119
1d	1k5jD00	D:16-118
1e	1k5jC00	C:16-118

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Nucleoplasmin] (6)

Family: Nucleoplasmin (6)

Xenopus laevis (African clawed frog) (4)

1a	Nucleoplasmin-1k5jE01	E:15-119
1b	Nucleoplasmin-1k5jE02	E:15-119
1c	Nucleoplasmin-1k5jE03	E:15-119
1d	Nucleoplasmin-1k5jE04	E:15-119
1e	Nucleoplasmin-1k5jE05	E:15-119

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E (NUPL_XENLA | P05221)

biological process
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007338	single fertilization	The union of male and female gametes to form a zygote.
cellular component
	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/Biological Unit
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	Sites
(no "Sites" information available for 1k5j)

	Cis Peptide Bonds
		Gly A:109 - Pro A:110	[ RasMol ]
		Gly B:109 - Pro B:110	[ RasMol ]
		Gly C:109 - Pro C:110	[ RasMol ]
		Gly D:109 - Pro D:110	[ RasMol ]
		Gly E:109 - Pro E:110	[ RasMol ]
		Pro A:98 - Pro A:99	[ RasMol ]
		Pro B:98 - Pro B:99	[ RasMol ]
		Pro C:98 - Pro C:99	[ RasMol ]
		Pro D:98 - Pro D:99	[ RasMol ]
		Pro E:98 - Pro E:99	[ RasMol ]

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	NUPL_XENLA \| P05221	:	1ee5 1ejy 2vtx 3ul1 4bpl

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