2J7J - JenaLib

Title :   INVARIANCE OF THE ZINC FINGER MODULE: A COMPARISON OF THE FREE STRUCTURE WITH THOSE IN NUCLEIC-ACID COMPLEXES

Authors :   D. Lu, A. Klug

Date :   10 Oct 06 (Deposition) - 09 Oct 07 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Zinc Finger Module, Alternative Initiation, Nuclear Protein, Phosphorylation, Hydrophobic Core, Zinc, Rna-Binding, Zinc-Finger, Dna-Binding, Transcription Regulation, Polymorphism, Transcription, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lu, A. Klug
Invariance Of The Zinc Finger Module: A Comparison Of The Free Structure With Those In Nucleic-Acid Complexes.
Proteins V. 67 508 2007
PubMed-ID: 17335000 | Reference-DOI: 10.1002/PROT.21289

Compounds

Molecule 1 - TRANSCRIPTION FACTOR IIIA
	Cell	:	OOCYTE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET13A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	ZINC FINGER 4-6, RESIDUES 127-210
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	FACTOR A, TFIIIA, S-TFIIIA/O-TFIIIA

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:4 , CYS A:9 , HIS A:22 , HIS A:26	BINDING SITE FOR RESIDUE ZN A1086
2	AC2	SOFTWARE	CYS A:34 , CYS A:39 , HIS A:52 , HIS A:56	BINDING SITE FOR RESIDUE ZN A1087
3	AC3	SOFTWARE	CYS A:61 , CYS A:67 , HIS A:80 , HIS A:85	BINDING SITE FOR RESIDUE ZN A1088
4	AC4	SOFTWARE	LYS A:11 , ARG A:48 , ARG A:51 , HOH A:2128	BINDING SITE FOR RESIDUE SO4 A1089

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Asymmetric Unit (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.	TF3A_XENLA	37-59 67-89 97-120 129-151 159-181 216-236 245-268 276-298	2	- - - A:4-26 A:34-56 - - -

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	TF3A_XENLA	37-59 67-89 97-120 129-151 159-181 216-236 245-268 276-298	4	- - - A:4-26 A:34-56 - - -

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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:85
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:85
                                   135       145       155       165       175       185       195       205     
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH 210
               SCOP domains d2j7ja1 A:1-28              d2j7ja2 A:29-57              d2j7ja3 A:58-85              SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhhhee.........ee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2j7j A   1 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH  85
                                    10        20        30        40        50        60        70        80

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

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (TF3A_XENLA | P03001)

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: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.
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: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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