1NLQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF DROSOPHILA NLP-CORE PROVIDES INSIGHT INTO PENTAMER FORMATION AND HISTONE BINDING

Authors :   V. M. H. Namboodiri, S. Dutta, I. V. Akey, J. F. Head, C. W. Akey

Date :   07 Jan 03 (Deposition) - 01 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Dnlp, Nucleoplasmin, Chaperone, Histone Binding, X-Ray Crystallography, Ligand Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. M. H. Namboodiri, S. Dutta, I. V. Akey, J. F. Head, C. W. Akey
The Crystal Structure Of Drosophila Nlp-Core Provides Insight Into Pentamer Formation And Histone Binding
Structure V. 11 175 2003
PubMed-ID: 12575937 | Reference-DOI: 10.1016/S0969-2126(03)00007-8
(for further references see the PDB file header)

Molecule 1 - NUCLEOPLASMIN-LIKE PROTEIN
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL CORE
	Gene	:	NLP OR CRP1 OR CG7917
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	DNLP, CHROMATIN DECONDENSATION PROTEIN 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:16 , HOH A:403 , HOH A:404 , HOH A:405 , HOH A:406 , HOH A:407	BINDING SITE FOR RESIDUE MG E 401
2	AC2	SOFTWARE	ASP E:16 , LEU E:90 , HOH E:426 , HOH E:440 , HOH E:463 , HOH E:464	BINDING SITE FOR RESIDUE MG A 402

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:95	-	Pro A:96
2	Gly B:95	-	Pro B:96
3	Gly C:95	-	Pro C:96
4	Gly D:95	-	Pro D:96
5	Gly E:95	-	Pro E:96

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

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

(no "Exon" information available for 1NLQ)

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:105
 aligned with NLP_DROME | Q27415 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:105
                                    12        22        32        42        52        62        72        82        92       102     
            NLP_DROME     3 EESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIKDD 107
               SCOP domains d1nlqa_ A: Chromatin decondensation protein 1 (Crp1, Nlp)                                                 SCOP domains
               CATH domains 1nlqA00 A:3-107  [code=2.60.120.340, no name defined]                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee..........eeeeeeeee........eeeeeeeehhhheeeeeeeee.....ee...eeee...eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1nlq A   3 EESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIKDD 107
                                    12        22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with NLP_DROME | Q27415 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:102
                                    13        23        33        43        53        63        73        83        93       103  
            NLP_DROME     4 ESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
               SCOP domains d1nlqb_ B: Chromati     n decondensation protein 1 (Crp1, Nlp)                                         SCOP domains
               CATH domains 1nlqB00 B:4-105  [c     ode=2.60.120.340, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....eeee..-----...eeeeeeeee........eeeeeeeehhhheeeeeeeee.....ee...eeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1nlq B   4 ESFYGVTLTAESDSVTWDV-----RGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
                                    13        |-    |   33        43        53        63        73        83        93       103  
                                             22    28

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with NLP_DROME | Q27415 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:102
                                    13        23        33        43        53        63        73        83        93       103  
            NLP_DROME     4 ESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
               SCOP domains d1nlqc_ C: Chromati      n decondensation protein 1 (Crp1, Nlp)                                        SCOP domains
               CATH domains 1nlqC00 C:4-105  [c      ode=2.60.120.340, no name defined]                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....eeee..------..eeeeeeeee........eeeeeeeehhhheeeeeeeee.....ee...eee....eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1nlq C   4 ESFYGVTLTAESDSVTWDV------GQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
                                    13        |-     |  33        43        53        63        73        83        93       103  
                                             22     29

Chain D from PDB  Type:PROTEIN  Length:94
 aligned with NLP_DROME | Q27415 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
            NLP_DROME     4 ESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNI 104
               SCOP domains d1nlqd_ D: Chromat       in decondensation protein 1 (Crp1, Nlp)                                      SCOP domains
               CATH domains 1nlqD00 D:4-104  [       code=2.60.120.340, no name defined]                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee.-------..eeeeeeeee........eeeeeeee....eeeeeeeee.....ee...eeee...eeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1nlq D   4 ESFYGVTLTAESDSVTWD-------GQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNI 104
                                    13       | -     |  33        43        53        63        73        83        93       103 
                                            21      29

Chain E from PDB  Type:PROTEIN  Length:98
 aligned with NLP_DROME | Q27415 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:102
                                    13        23        33        43        53        63        73        83        93       103  
            NLP_DROME     4 ESFYGVTLTAESDSVTWDVDEDYARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
               SCOP domains d1nlqe_ E: Chromati    n decondensation protein 1 (Crp1, Nlp)                                          SCOP domains
               CATH domains 1nlqE00 E:4-105  [c    ode=2.60.120.340, no name defined]                                              CATH domains
           Pfam domains (1) Nucleoplasmin-1nlqE    01 E:4-105                                                                      Pfam domains (1)
           Pfam domains (2) Nucleoplasmin-1nlqE    02 E:4-105                                                                      Pfam domains (2)
           Pfam domains (3) Nucleoplasmin-1nlqE    03 E:4-105                                                                      Pfam domains (3)
           Pfam domains (4) Nucleoplasmin-1nlqE    04 E:4-105                                                                      Pfam domains (4)
           Pfam domains (5) Nucleoplasmin-1nlqE    05 E:4-105                                                                      Pfam domains (5)
         Sec.struct. author .eeeeeee.....eeee..----....eeeeeeeee........eeeeeeeehhhheeeeeeeee.....ee...eeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1nlq E   4 ESFYGVTLTAESDSVTWDV----ARGQKLVIKQILLGAEAKENEFNVVEVNTPKDSVQIPIAVLKAGETRAVNPDVEFYESKVTFKLIKGSGPVYIHGHNIK 105
                                    13        |-   |    33        43        53        63        73        83        93       103  
                                             22   27

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: Chromatin decondensation protein 1 (Crp1, Nlp) (1)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (1)

1a	d1nlqa_	A:
1b	d1nlqb_	B:
1c	d1nlqc_	C:
1d	d1nlqd_	D:
1e	d1nlqe_	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)

Fruit fly (Drosophila melanogaster) (1)

1a	1nlqE00	E:4-105
1b	1nlqB00	B:4-105
1c	1nlqC00	C:4-105
1d	1nlqA00	A:3-107
1e	1nlqD00	D:4-104

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Nucleoplasmin (6)

Drosophila melanogaster (Fruit fly) (1)

1a	Nucleoplasmin-1nlqE01	E:4-105
1b	Nucleoplasmin-1nlqE02	E:4-105
1c	Nucleoplasmin-1nlqE03	E:4-105
1d	Nucleoplasmin-1nlqE04	E:4-105
1e	Nucleoplasmin-1nlqE05	E:4-105

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E (NLP_DROME | Q27415)

molecular function
	GO:0042623	ATPase activity, coupled	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
biological process
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0016584	nucleosome positioning	Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another.
	GO:0035041	sperm chromatin decondensation	Unwinding of the condensed nuclear chromatin of an inactive sperm nucleus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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		Gly C:95 - Pro C:96	[ RasMol ]
		Gly D:95 - Pro D:96	[ RasMol ]
		Gly E:95 - Pro E:96	[ RasMol ]

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1k5j	A RELATED HISTONE CHAPERONE FROM XENOPUS LAEVIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 5)

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