1UN6 | PR0205 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION

Authors :   D. Lu, M. A. Searles, A. Klug

Date :   04 Sep 03 (Deposition) - 20 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : B,C,D,E,F
Biol. Unit 1: C,E  (1x)
Biol. Unit 2: B,D,F  (1x)

Keywords :   Rna-Binding Protein/Rna, Complex(Zinc Finger/Rna), Tfiiia, 5S Ribosomal Rna, Zinc Finger, Rna-Protein Complex, X. Laevis, Transcription Regulation, Rna-Binding, Dna- Binding, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lu, M. A. Searles, A. Klug
Crystal Structure Of A Zinc-Finger-Rna Complex Reveals Two Modes Of Molecular Recognition
Nature V. 426 96 2003
PubMed-ID: 14603324 | Reference-DOI: 10.1038/NATURE02088
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION FACTOR IIIA
	Cell	:	OOCYTE
	Chains	:	B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET13A3F
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	FINGERS 4,5 AND 6, RESIDUES 127 - 212 UNDER SWISSPROT NUMBERING FOR SOMATIC TFIIIA
	Organ	:	OVARY
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	TFIIIA, FACTOR A, S-TFIIIA/O-TFIIIA

Molecule 2 - 5S RIBOSOMAL RNA
	Cell	:	OOCYTE
	Chains	:	E, F
	Fragment	:	CENTRAL REGION, NUCLEOTIDES 4 - 15,64 -82,94-115, PLUS TWO TETRALOOPS JOINING 15 - 64 AND 82 - 94 RESPECTIVELY
	Organ	:	OVARY
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Other Details	:	UACG TETRALOOP LINKING NUCLEOTIDES 15 AND 64, GAAA TETRALOOP LINKING NUCLEOTIDES 82 AND 94
	Other Details - Source	:	IN VITRO TRANSCRIPTION TO PRODUCE THE RNA

		1	2	3	4	5
Asymmetric Unit	:	B	C	D	E	F
Biological Unit 1 (1x)	:		C		E
Biological Unit 2 (1x)	:	B		D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 21)

No.	Name	Count	Type	Full Name
1	MG	13	Ligand/Ion	MAGNESIUM ION
2	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS B:107 , CYS B:112 , HIS B:125 , HIS B:129	BINDING SITE FOR RESIDUE ZN B 204
02	AC2	SOFTWARE	CYS B:137 , CYS B:142 , HIS B:155 , HIS B:159	BINDING SITE FOR RESIDUE ZN B 205
03	AC3	SOFTWARE	CYS B:164 , CYS B:170 , HIS B:183 , HIS B:188	BINDING SITE FOR RESIDUE ZN B 206
04	AC4	SOFTWARE	CYS B:164 , ASP B:168 , CYS B:170	BINDING SITE FOR RESIDUE MG B 306
05	AC5	SOFTWARE	PRO B:163 , LYS B:165	BINDING SITE FOR RESIDUE MG B 307
06	AC6	SOFTWARE	CYS B:137 , HIS B:139 , CYS B:142	BINDING SITE FOR RESIDUE MG B 308
07	AC7	SOFTWARE	CYS C:107 , CYS C:112 , HIS C:125 , HIS C:129	BINDING SITE FOR RESIDUE ZN C 204
08	AC8	SOFTWARE	CYS C:137 , CYS C:142 , HIS C:155 , HIS C:159	BINDING SITE FOR RESIDUE ZN C 205
09	AC9	SOFTWARE	CYS C:164 , CYS C:170 , HIS C:183 , HIS C:188	BINDING SITE FOR RESIDUE ZN C 206
10	BC1	SOFTWARE	G E:7	BINDING SITE FOR RESIDUE MG C 342
11	BC2	SOFTWARE	CYS C:137 , HIS C:139 , CYS C:142	BINDING SITE FOR RESIDUE MG C 344
12	BC3	SOFTWARE	CYS D:137 , CYS D:142 , HIS D:155 , HIS D:159	BINDING SITE FOR RESIDUE ZN D 205
13	BC4	SOFTWARE	CYS D:164 , CYS D:170 , HIS D:183 , HIS D:188	BINDING SITE FOR RESIDUE ZN D 206
14	BC5	SOFTWARE	G E:113	BINDING SITE FOR RESIDUE MG E 341
15	BC6	SOFTWARE	G E:97 , G E:98	BINDING SITE FOR RESIDUE MG E 343
16	BC7	SOFTWARE	G F:98	BINDING SITE FOR RESIDUE MG F 302
17	BC8	SOFTWARE	G F:114	BINDING SITE FOR RESIDUE MG F 303
18	BC9	SOFTWARE	G F:110	BINDING SITE FOR RESIDUE MG F 304
19	CC1	SOFTWARE	G F:70 , G F:71	BINDING SITE FOR RESIDUE MG F 305
20	CC2	SOFTWARE	G F:66 , C F:67 , G F:108 , U F:109	BINDING SITE FOR RESIDUE MG F 309

(no "SS Bond" information available for 1UN6)

(no "Cis Peptide Bond" information available for 1UN6)

(no "SAP(SNP)/Variant" information available for 1UN6)

Asymmetric Unit (1, 5)

	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	5	- - - B:107-129 C:107-129 B:137-159 C:137-159 D:137-159 - - -

Biological Unit 1 (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	- - - - C:107-129 - C:137-159 - - - -

Biological Unit 2 (1, 3)

	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	3	- - - B:107-129 - B:137-159 - D:137-159 - - -

(no "Exon" information available for 1UN6)

Asymmetric 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 B from PDB  Type:PROTEIN  Length:87
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:87
                                   135       145       155       165       175       185       195       205       
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6b1 B:104-131           d1un6b2 B:132-160            d1un6b3 B:161-190              SCOP domains
               CATH domains 1un6B01 B:104-132            1un6B02 B:133-161            1un6B03 B:162-190             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1un6 B 104 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   113       123       133       143       153       163       173       183

Chain C from PDB  Type:PROTEIN  Length:87
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:87
                                   135       145       155       165       175       185       195       205       
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6c1 C:104-131           d1un6c2 C:132-160            d1un6c3 C:161-190              SCOP domains
               CATH domains 1un6C01 C:104-132            1un6C02 C:133-161            1un6C03 C:162-190             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1un6 C 104 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   113       123       133       143       153       163       173       183

Chain D from PDB  Type:PROTEIN  Length:58
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:58
                                   164       174       184       194       204        
           TF3A_XENLA   155 LPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6d1 D:133-160           d1un6d2 D:161-190              SCOP domains
               CATH domains 1un6D01 D:133-159          1un6D02 D:160-190               CATH domains
           Pfam domains (1) --zf-C2H2-1un6D01 D:135-159------------------------------- Pfam domains (1)
           Pfam domains (2) --zf-C2H2-1un6D02 D:135-159------------------------------- Pfam domains (2)
           Pfam domains (3) --zf-C2H2-1un6D03 D:135-159------------------------------- Pfam domains (3)
           Pfam domains (4) --zf-C2H2-1un6D04 D:135-159------------------------------- Pfam domains (4)
           Pfam domains (5) --zf-C2H2-1un6D05 D:135-159------------------------------- Pfam domains (5)
         Sec.struct. author ..ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1un6 D 133 LPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   142       152       162       172       182

Chain E from PDB  Type:RNA  Length:61
                                                                                             
                 1un6 E   4 GCCGGCCACACCUACGGGGCCUGGUUAGUACCUGGGAAACCUGGGAAUACCAGGUGCCGGC 115
                                    13     || 67        77        94       104       114 
                                          19|                    86|                     
                                           64                     94

Chain F from PDB  Type:RNA  Length:61
                                                                                             
                 1un6 F   4 GCCGGCCACACCUACGGGGCCUGGUUAGUACCUGGGAAACCUGGGAAUACCAGGUGCCGGC 115
                                    13     || 67        77        94       104       114 
                                          19|                    86|                     
                                           64                     94

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 '\|'

Asymmetric Unit

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: Transcription factor IIIA, TFIIIA (4)

African clawed frog (Xenopus laevis) [TaxId: 8355] (4)

1a	d1un6b1	B:104-131
1b	d1un6b2	B:132-160
1c	d1un6b3	B:161-190
1d	d1un6c1	C:104-131
1e	d1un6c2	C:132-160
1f	d1un6c3	C:161-190
1g	d1un6d1	D:133-160
1h	d1un6d2	D:161-190

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: Classic Zinc Finger (45)

African clawed frog (Xenopus laevis) (2)

1a	1un6B02	B:133-161
1b	1un6C02	C:133-161
1c	1un6D01	D:133-159
1d	1un6D02	D:160-190
1e	1un6B03	B:162-190
1f	1un6C03	C:162-190
1g	1un6B01	B:104-132
1h	1un6C01	C:104-132

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C2H2-zf (71)

Family: zf-C2H2 (11)

Xenopus laevis (African clawed frog) (3)

1a	zf-C2H2-1un6D01	D:135-159
1b	zf-C2H2-1un6D02	D:135-159
1c	zf-C2H2-1un6D03	D:135-159
1d	zf-C2H2-1un6D04	D:135-159
1e	zf-C2H2-1un6D05	D:135-159

Asymmetric Unit(hide GO term definitions)

Chain B,C,D (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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	RNA: green surface; protein: brown surface; metal ions: spacefill (Mg2+: green, Zn2+: violet); black background [ mono GIF format \| stereo GIF format ]
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	1un6
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	TF3A_XENLA \| P03001	:	1tf3 1tf6 2hgh 2j7j

1tf3	TFIIIA FINGER 1-3 BOUND TO DEOXYRIBONUCLEIC ACID, NMR, 22 STRUCTURES
1tf6	CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RIBONUCLEIC ACID GENE INTERNAL CONTROL REGION

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Ligands, Modified Residues, Ions (2, 21)

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