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NMR Structure - model 1

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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

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Description

Title :   SOLUTION STRUCTURE OF THE FIRST ZINC-FINGER DOMAIN FROM ZNF265

Authors :   C. A. Plambeck, K. Fairley, A. H. Y. Kwan, B. J. Westman, D. Adams, B. Morris, J. P. Mackay

Date :   15 Oct 02 (Deposition) - 22 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Zinc Finger, Rna Splicing, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Plambeck, A. H. Y. Kwan, D. J. Adams, B. J. Westman, L. Van Der Weyden, R. L. Medcalf, B. J. Morris, J. P. Mackay
The Structure Of The Zinc Finger Domain From Human Splicing Factor Znf265 Fold
J. Biol. Chem. V. 278 22805 2003
PubMed-ID: 12657633 | Reference-DOI: 10.1074/JBC.M301896200
(for further references see the PDB file header)

Compounds

Molecule 1 - ZNF265
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZNF265-F1
	Gene	:	ZNF265
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZINC FINGER PROTEIN 265

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Sites (1, 1)

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:17 , CYS A:22 , CYS A:33 , CYS A:36	BINDING SITE FOR RESIDUE ZN A 46

SS Bonds (0, 0)

(no "SS Bond" information available for 1N0Z)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1N0Z)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1N0Z)

PROSITE Motifs (2, 2)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_RANBP2_2	PS50199	Zinc finger RanBP2 type profile.	ZRAB2_HUMAN	9-40 65-94	1	A:11-42 -
2	ZF_RANBP2_1	PS01358	Zinc finger RanBP2-type signature.	ZRAB2_HUMAN	13-34 69-88	1	A:15-36 -

Exons (3, 3)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000370920	1a	ENSE00001954996	chr1:71546980-71546623	358	ZRAB2_HUMAN	1-19	19	1	A:3-21	19
1.2	ENST00000370920	2	ENSE00000903869	chr1:71544391-71544339	53	ZRAB2_HUMAN	19-37	19	1	A:21-39	19
1.3	ENST00000370920	3	ENSE00000903868	chr1:71544248-71544140	109	ZRAB2_HUMAN	37-73	37	1	A:39-45 (gaps)	16
1.4	ENST00000370920	4	ENSE00000903867	chr1:71542560-71542478	83	ZRAB2_HUMAN	73-101	29	0	-	-
1.5	ENST00000370920	5	ENSE00000903866	chr1:71538231-71538155	77	ZRAB2_HUMAN	101-126	26	0	-	-
1.6	ENST00000370920	6	ENSE00000903865	chr1:71537938-71537804	135	ZRAB2_HUMAN	127-171	45	0	-	-
1.7	ENST00000370920	7	ENSE00000995752	chr1:71536679-71536510	170	ZRAB2_HUMAN	172-228	57	0	-	-
1.8b	ENST00000370920	8b	ENSE00000995751	chr1:71535045-71534959	87	ZRAB2_HUMAN	228-257	30	0	-	-
1.9d	ENST00000370920	9d	ENSE00000903863	chr1:71532617-71532459	159	ZRAB2_HUMAN	257-310	54	0	-	-
1.10f	ENST00000370920	10f	ENSE00001867543	chr1:71530820-71528974	1847	ZRAB2_HUMAN	310-330	21	0	-	-

Sequences/Alignments

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:45
 aligned with ZRAB2_HUMAN | O95218 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:54
                              1                                                   
                              |      8        18        28        38        48    
           ZRAB2_HUMAN    - --MSTKNFRVSDGDWICPDKKCGNVNFARRTSCNRCGREKTTEAKMMKAGGTEI 52
               SCOP domains d1n0za_ A: Znf265, first zinc-finger domai       n     SCOP domains
               CATH domains 1n0zA00 A:1-45                                         CATH domains
               Pfam domains ----------zf-RanBP-1n0zA01 A:11-40      -------------- Pfam domains
         Sec.struct. author ..........................................-------.--.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------ZF_RANBP2_2  PDB: A:11-42       ------------ PROSITE (1)
                PROSITE (2) --------------ZF_RANBP2_1           ------------------ PROSITE (2)
           Transcript 1 (1) --Exon 1.1a          -----------------Exon 1.3         Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2           --------------- Transcript 1 (2)
                  1n0z A  1 GSMSTKNFRVSDGDWICPDKKCGNVNFARRTSCDRCGREKTT-------G--PI 45
                                    10        20        30        40 |      43  | 
                                                                    42      43 44

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 (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Ran binding protein zinc finger-like (16)

Family: Ran binding protein zinc finger-like (16)

Protein domain: Znf265, first zinc-finger domain (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1n0za_

CATH Domains (1, 1)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: ZNF265 like (1)

Homologous Superfamily: Znf265, first zinc-finger domain (1)

Human (Homo sapiens) (1)

1n0zA00

A:1-45

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Zn_Beta_Ribbon (109)

Family: zf-RanBP (6)

Homo sapiens (Human) (5)

zf-RanBP-1n0zA01

A:11-40

Gene Ontology (10, 10)

NMR Structure(hide GO term definitions)

Chain A (ZRAB2_HUMAN | O95218)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	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.

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Related Entries

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	ZRAB2_HUMAN \| O95218	:	2k1p 3g9y

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