4A75 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXATHYMIDINE.

Authors :   F. Mayr, A. Schuetz, N. Doege, U. Heinemann

Date :   11 Nov 11 (Deposition) - 05 Sep 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H  (1x)

Keywords :   Chaperone-Dna Complex, Chaperone, Dna/Rna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Mayr, A. Schutz, N. Doge, U. Heinemann
The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna.
Nucleic Acids Res. V. 40 7492 2012
PubMed-ID: 22570413 | Reference-DOI: 10.1093/NAR/GKS355

Molecule 1 - LIN28 COLD SHOCK DOMAIN
	Chains	:	A, C, E, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	WESTERN CLAWED FROG
	Organism Scientific	:	XENOPUS (SILURANA) TROPICALIS
	Organism Taxid	:	8364

*Molecule 2 - 5'-D(TPTPTPTPTPTP)-3'*
	Chains	:	B, D, F, H
	Synonym	:	HEXATHYMIDINE
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SCN	2	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SCN	-1	Ligand/Ion	THIOCYANATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	SCN	-1	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DT H:4 , DT H:5	BINDING SITE FOR RESIDUE SCN A1114
2	AC2	SOFTWARE	THR E:89 , ARG E:101 , THR G:89	BINDING SITE FOR RESIDUE SCN E1114

(no "SS Bond" information available for 4A75)

(no "Cis Peptide Bond" information available for 4A75)

(no "SAP(SNP)/Variant" information available for 4A75)

(no "PROSITE Motif" information available for 4A75)

(no "Exon" information available for 4A75)

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 A from PDB  Type:PROTEIN  Length:89
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:105
                                    18        28        38        48        58        68        78        88        98       108     
         B4F6I0_XENTR     9 GTREEQGKLPEQEEEEEEDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4                a75a_ A: automated matches                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4a75 A  25 GS----------------DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                             |       -        28        38        48        58        68        78        88        98       108     
                             |               27                                                                                      
                            26

Chain B from PDB  Type:DNA  Length:5
                                     
                 4a75 B   3 TTTTT   7

Chain C from PDB  Type:PROTEIN  Length:87
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:87
                                    36        46        56        66        76        86        96       106       
         B4F6I0_XENTR    27 DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a75c_ C: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4a75 C  27 DPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    36        46        56        66        76        86        96       106

Chain D from PDB  Type:DNA  Length:6
                                      
                 4a75 D   2 TTTTTT   7

Chain E from PDB  Type:PROTEIN  Length:88
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:88
                                    35        45        55        65        75        85        95       105        
         B4F6I0_XENTR    26 EDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a75e_ E: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4a75 E  26 SDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    35        45        55        65        75        85        95       105

Chain F from PDB  Type:DNA  Length:5
                                     
                 4a75 F   3 TTTTT   7

Chain G from PDB  Type:PROTEIN  Length:88
 aligned with B4F6I0_XENTR | B4F6I0 from UniProtKB/TrEMBL  Length:253

    Alignment length:88
                                    35        45        55        65        75        85        95       105        
         B4F6I0_XENTR    26 EDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
               SCOP domains d4a75g_ G: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeee................eeeeeeeee..eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4a75 G  26 SDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGN 113
                                    35        45        55        65        75        85        95       105

Chain H from PDB  Type:DNA  Length:6
                                      
                 4a75 H   2 TTTTTT   7

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(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: automated matches (46)

Protein domain: automated matches (46)

Xenopus (Silurana) tropicalis [TaxId: 8364] (3)

1a	d4a75a_	A:
1b	d4a75c_	C:
1c	d4a75e_	E:
1d	d4a75g_	G:

(no "CATH Domain" information available for 4A75)

(no "Pfam Domain" information available for 4A75)

Asymmetric Unit(hide GO term definitions)

Chain A,C,E,G (B4F6I0_XENTR | B4F6I0)

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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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	Cis Peptide Bonds
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Biological Units
	Complete Structure
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		Biological Unit 4	[ Jena3D ]

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	B4F6I0_XENTR \| B4F6I0	:	3ulj 4a76 4alp

4a76	THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEPTATHYMIDINE
4alp	THE LIN28B COLD SHOCK DOMAIN IN COMPLEX WITH HEXAURIDINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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