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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE FIFTH COLD-SHOCK DOMAIN OF THE HUMAN KIAA0885 PROTEIN (UNR PROTEIN)

Authors :   A. K. Goroncy, N. Tochio, T. Tomizawa, S. Koshiba, S. Watanabe, T. Harad T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics In (Rsgi)

Date :   05 Apr 07 (Deposition) - 08 Apr 08 (Release) - 01 Sep 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Cell-Free Protein Synthesis, Beta-Barrel, Translational Regulation, Rna Chaperone, Rna/Dna Binding, Qb Fold, Greek-Key Topology, Unr Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Goroncy, S. Koshiba, N. Tochio, T. Tomizawa, M. Inoue, S. Watanabe, T. Harada, A. Tanaka, O. Ohara, T. Kigawa, S. Yokoyama
The Nmr Solution Structures Of The Five Constituent Cold-Shock Domains (Csd) Of The Human Unr (Upstream Of N-Ras) Protein.
J. Struct. Funct. Genom. V. 11 181 2010
PubMed-ID: 20213426 | Reference-DOI: 10.1007/S10969-010-9081-Z

Molecule 1 - COLD SHOCK DOMAIN-CONTAINING PROTEIN E1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P070129-03
	Expression System Vector Type	:	PLASMID
	Fragment	:	FIFTH COLD-SHOCK DOMAIN
	Gene	:	KIAA0885
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	UNR PROTEIN, N-RAS UPSTREAM GENE PROTEIN

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YTV)

(no "Site" information available for 2YTV)

(no "SS Bond" information available for 2YTV)

(no "Cis Peptide Bond" information available for 2YTV)

(no "SAP(SNP)/Variant" information available for 2YTV)

(no "PROSITE Motif" information available for 2YTV)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2h	ENST00000358528	2h	ENSE00001828752	chr1:115300585-115300546	40	CSDE1_HUMAN	-	0	0	-	-
1.4b	ENST00000358528	4b	ENSE00001337441	chr1:115292828-115292442	387	CSDE1_HUMAN	-	0	0	-	-
1.8c	ENST00000358528	8c	ENSE00001713511	chr1:115282511-115282313	199	CSDE1_HUMAN	1-67	67	0	-	-
1.9b	ENST00000358528	9b	ENSE00001151258	chr1:115280693-115280584	110	CSDE1_HUMAN	67-103	37	0	-	-
1.10	ENST00000358528	10	ENSE00000784321	chr1:115280184-115280092	93	CSDE1_HUMAN	104-134	31	0	-	-
1.11	ENST00000358528	11	ENSE00002166908	chr1:115279476-115279379	98	CSDE1_HUMAN	135-167	33	0	-	-
1.12	ENST00000358528	12	ENSE00001151239	chr1:115277144-115277063	82	CSDE1_HUMAN	167-194	28	0	-	-
1.13	ENST00000358528	13	ENSE00000800122	chr1:115276738-115276610	129	CSDE1_HUMAN	195-237	43	0	-	-
1.14b	ENST00000358528	14b	ENSE00000784325	chr1:115276478-115276353	126	CSDE1_HUMAN	238-279	42	0	-	-
1.15	ENST00000358528	15	ENSE00000800120	chr1:115275437-115275225	213	CSDE1_HUMAN	280-350	71	0	-	-
1.16	ENST00000358528	16	ENSE00001386496	chr1:115273269-115273129	141	CSDE1_HUMAN	351-397	47	0	-	-
1.17	ENST00000358528	17	ENSE00000784333	chr1:115273043-115272879	165	CSDE1_HUMAN	398-452	55	0	-	-
1.18	ENST00000358528	18	ENSE00000800117	chr1:115269711-115269604	108	CSDE1_HUMAN	453-488	36	0	-	-
1.19a	ENST00000358528	19a	ENSE00001450278	chr1:115269007-115268832	176	CSDE1_HUMAN	489-547	59	0	-	-
1.20	ENST00000358528	20	ENSE00001151209	chr1:115267954-115267842	113	CSDE1_HUMAN	547-585	39	0	-	-
1.21b	ENST00000358528	21b	ENSE00001151205	chr1:115266623-115266504	120	CSDE1_HUMAN	585-625	41	0	-	-
1.22b	ENST00000358528	22b	ENSE00001151196	chr1:115263338-115263160	179	CSDE1_HUMAN	625-684	60	1	A:1-19 (gaps)	36
1.23	ENST00000358528	23	ENSE00001196939	chr1:115262363-115262200	164	CSDE1_HUMAN	685-739	55	1	A:20-74	55
1.24b	ENST00000358528	24b	ENSE00000784340	chr1:115261366-115261234	133	CSDE1_HUMAN	739-783	45	1	A:74-78 (gaps)	45
1.25f	ENST00000358528	25f	ENSE00001374597	chr1:115260837-115259538	1300	CSDE1_HUMAN	784-798	15	1	A:79-79	1

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:79
 aligned with CSDE1_HUMAN | O75534 from UniProtKB/Swiss-Prot  Length:798

    Alignment length:136
                                   658       668       678       688       698       708       718       728       738       748       758       768       778      
          CSDE1_HUMAN   649 GESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASAPRLMVLRQPRGPDNSMG 784
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------CSD-2ytvA01 A:9-73                                               ---------------------------------------------- Pfam domains
         Sec.struct. author ...--------..---------.....eeeee....eeee.........eeee..............eee...ee......ee....ee..-..---------------------------------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.22b  PDB: A:1-19 (gaps)      Exon 1.23  PDB: A:20-74 UniProt: 685-739               --------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.24b  PDB: A:74-78 (gaps)              - Transcript 1 (2)
                 2ytv A   1 GSS--------GS---------SGLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVS-GP---------------------------------------SSG  79
                              |      - ||      -  |     13        23        33        43        53        63        73| ||     -         -         -         -   |  
                              3        4|         6                                                                  74 ||                                      77  
                                        5                                                                              75|                                          
                                                                                                                        76

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2YTV)

(no "CATH Domain" information available for 2YTV)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: CSD (10)

Homo sapiens (Human) (5)

CSD-2ytvA01

A:9-73

NMR Structure(hide GO term definitions)

Chain A (CSDE1_HUMAN | O75534)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	GO:0070966	nuclear-transcribed mRNA catabolic process, no-go decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0070937	CRD-mediated mRNA stability complex	A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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