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Description

Title :   SOLUTION STRUCTURE OF THE C2H2 TYPE ZINC FINGER (REGION 612-644) OF HUMAN ZINC FINGER PROTEIN 28 HOMOLOG

Authors :   T. Tomizawa, N. Tochio, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Mar 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Zf-C2H2, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tochio, T. Tomizawa, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama
Solution Structure Of The C2H2 Type Zinc Finger (Region 612-644) Of Human Zinc Finger Protein 28 Homolog
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - ZINC FINGER PROTEIN 28 HOMOLOG
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P061225-33
	Expression System Vector Type	:	PLASMID
	Fragment	:	ZF-C2H2 DOMAIN
	Gene	:	ZFP28
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	ZFP-28, KRUEPPEL-LIKE ZINC FINGER FACTOR X6

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:15 , CYS A:18 , HIS A:31 , HIS A:35	BINDING SITE FOR RESIDUE ZN A 201

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024190	A	620	V	ZFP28_HUMAN	Polymorphism	10409531	A	A	16	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 2)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	ZFP28_HUMAN	422-442 450-470 478-499 507-527 535-555 563-583 591-611 619-639 647-667 675-695 703-723 731-751 759-779 787-807	2	- - - - - - - A:15-35 - A:46-46 - - - -

Exons (1, 1)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000301318	1	ENSE00000728674	chr19:57050317-57050595	279	ZFP28_HUMAN	1-70	70	0	-	-
1.2	ENST00000301318	2	ENSE00001319353	chr19:57050994-57051085	92	ZFP28_HUMAN	70-100	31	0	-	-
1.3	ENST00000301318	3	ENSE00001638838	chr19:57058877-57059003	127	ZFP28_HUMAN	101-143	43	0	-	-
1.4	ENST00000301318	4	ENSE00000728686	chr19:57059176-57059271	96	ZFP28_HUMAN	143-175	33	0	-	-
1.5	ENST00000301318	5	ENSE00000728690	chr19:57060327-57060490	164	ZFP28_HUMAN	175-229	55	0	-	-
1.6	ENST00000301318	6	ENSE00000728695	chr19:57061436-57061550	115	ZFP28_HUMAN	230-268	39	0	-	-
1.7	ENST00000301318	7	ENSE00000728701	chr19:57061879-57061974	96	ZFP28_HUMAN	268-300	33	0	-	-
1.8	ENST00000301318	8	ENSE00001290596	chr19:57065053-57068169	3117	ZFP28_HUMAN	300-868	569	1	A:1-46 (gaps)	135

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:46
 aligned with ZFP28_HUMAN | Q8NHY6 from UniProtKB/Swiss-Prot  Length:868

    Alignment length:135
                                   554       564       574       584       594       604       614       624       634       644       654       664       674     
          ZFP28_HUMAN   545 GSSLTVHQRIHTGEKPYECDVCRKAFSHHASLTQHQRVHSGEKPFKCKECGKAFRQNIHLASHLRIHTGEKPFECAECGKSFSISSQLATHQRIHTGEKPYECKVCSKAFTQKAHLAQHQKTHTGEKPYECKECG 679
               SCOP domains -------------------------------------------------------------------d2emja1 A:8-35              ---------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---------..-------------------------..--------------------------.....ee......ee.hhhhhhhhhhhhh....-----------------------..--.----... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZINC_FINGER-------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_ PROSITE
               Transcript 1 Exon 1.8  PDB: A:1-46 (gaps) UniProt: 300-868 [INCOMPLETE]                                                                              Transcript 1
                 2emj A   1 GSS---------GS-------------------------SG--------------------------TGEKPFECAECGKSFSISSQLATHQRIHTGEKP-----------------------SG--P----SSG  46
                              |      -  ||     -         -         6|        -         -       |10        20        30        40         -         -   ||  | -  |  
                              3         4|                         6|                          8                              40                      41| 43   44  
                                         5                          7                                                                                  42

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: beta-beta-alpha zinc fingers (183)

Superfamily: beta-beta-alpha zinc fingers (183)

Family: Classic zinc finger, C2H2 (162)

Protein domain: automated matches (93)

Human (Homo sapiens) [TaxId: 9606] (92)

d2emja1

A:8-35

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2EMJ)

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (ZFP28_HUMAN | Q8NHY6)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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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UniProtKB/Swiss-Prot
	ZFP28_HUMAN \| Q8NHY6	:	2em2 2em3 2em4 2emk 2eml 2en9 2enh 2eoh 2ep0 2epx 2epz 2ytm

Related Entries Specified in the PDB File

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