1SQW - JenaLib

Title :   CRYSTAL STRUCTURE OF KD93, A NOVEL PROTEIN EXPRESSED IN THE HUMAN PRO

Authors :   J. F. Liu, X. Q. Wang, Z. X. Wang, J. R. Chen, T. Jiang, X. M. An, W. R. Chan, D. C. Liang

Date :   19 Mar 04 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Pua, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Liu, X. Q. Wang, Z. X. Wang, J. R. Chen, T. Jiang, X. M. An, W. R. Chang, D. C. Liang
Crystal Structure Of Kd93, A Novel Protein Expressed In Human Hematopoietic Stem/Progenitor Cells.
J. Struct. Biol. V. 148 370 2004
PubMed-ID: 15522784 | Reference-DOI: 10.1016/J.JSB.2004.06.010
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (5, 5)

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000254940	1a	ENSE00001912636	chr16:69373343-69373788	446	NIP7_HUMAN	1-19	19	1	A:1-19	19
1.2	ENST00000254940	2	ENSE00000904600	chr16:69373909-69373995	87	NIP7_HUMAN	19-48	30	1	A:19-48	30
1.3	ENST00000254940	3	ENSE00000904602	chr16:69374097-69374235	139	NIP7_HUMAN	48-94	47	1	A:48-94	47
1.4	ENST00000254940	4	ENSE00000904606	chr16:69375083-69375223	141	NIP7_HUMAN	95-141	47	1	A:95-141	47
1.5b	ENST00000254940	5b	ENSE00001872045	chr16:69375436-69377014	1579	NIP7_HUMAN	142-180	39	1	A:142-176	35

Sequences/Alignments

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:176
 aligned with NIP7_HUMAN | Q9Y221 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
           NIP7_HUMAN     1 MRPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKFRLHVTALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHE 176
               SCOP domains d1sqwa2 A:1-94 Nip7p homolog, N-terminal domain                                               d1sqwa1 A:95-176 Nip7p homolog, C-terminal domain                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains UPF0113-1sqwA01 A:1-175                                                                                                                                                        - Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhh..hhhhhee..eeeeeeee..eeeeeehhhhhh....hhhhhhhhheeeeee.....eee...hhhhhhhhh..eeeehhhhhhhhh....ee...eeee........eeeeee....eeeeeee..hhhhhhhh....eeeeeeee.hhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------------------PUA  PDB: A:94-170 UniProt: 94-170                                           ------ PROSITE
           Transcript 1 (1) Exon 1.1a          ----------------------------Exon 1.3  PDB: A:48-94 UniProt: 48-94          Exon 1.4  PDB: A:95-141 UniProt: 95-141        Exon 1.5b  PDB: A:142-176           Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.2  PDB: A:19-48        -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1sqw A   1 MRPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKFRLHVTALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHE 176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NIP7_HUMAN | Q9Y221)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0042255	ribosome assembly	The aggregation, arrangement and bonding together of the mature ribosome and of its subunits.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
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: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.

Visualization

Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 1sqw)

	Sites
(no "Sites" information available for 1sqw)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sqw)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1sqw
		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
	NIP7_HUMAN \| Q9Y221
		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

Description