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Description

Title :   CRYSTAL STRUCTURE OF BS-CSPB IN COMPLEX WITH R(GUCUUUA)

Authors :   R. Sachs, K. E. A. Max, U. Heinemann

Date :   27 Oct 10 (Deposition) - 21 Sep 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.38

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

Keywords :   Beta Barrel, Protein-Rna Complex, Cold Shock Response, Transcription Regulation, Translation Regulation, Ob Fold, Cold Shock Domain, Rna/Dna Binding, Single-Stranded Rna And Dna, Cytosol, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sachs, K. E. Max, U. Heinemann, J. Balbach
Rna Single Strands Bind To A Conserved Surface Of The Major Cold Shock Protein In Crystals And Solution.
Rna V. 18 65 2012
PubMed-ID: 22128343 | Reference-DOI: 10.1261/RNA.02809212

Compounds

Molecule 1 - COLD SHOCK PROTEIN CSPB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU09100, CSPA, CSPB
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	MAJOR COLD SHOCK PROTEIN

Molecule 2 - HEXARIBONUCLEOTIDE (RGUCUUUA)
	Chains	:	R
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2	3
Asymmetric Unit	:	A	B	R
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B	R

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:35 , GLU A:36 , GLY A:37 , LYS A:39	BINDING SITE FOR RESIDUE NA A 68
2	AC2	SOFTWARE	HOH A:92 , HOH A:115 , HOH A:122 , HOH A:127 , HOH A:131 , HOH A:160	BINDING SITE FOR RESIDUE MG A 69

SS Bonds (0, 0)

(no "SS Bond" information available for 3PF4)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3PF4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CSPB_BACSU_001 *	F	17	L	CSPB_BACSU	---	---	A/B	F	17	L
2	UniProt	VAR_CSPB_BACSU_002 *	G	44	S	CSPB_BACSU	---	---	A/B	G	44	S
3	UniProt	VAR_CSPB_BACSU_003 *	A	46	S	CSPB_BACSU	---	---	A/B	A	46	S
	* ID not provided by source

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CSPB_BACSU_001 *	F	17	L	CSPB_BACSU	---	---	A	F	17	L
2	UniProt	VAR_CSPB_BACSU_002 *	G	44	S	CSPB_BACSU	---	---	A	G	44	S
3	UniProt	VAR_CSPB_BACSU_003 *	A	46	S	CSPB_BACSU	---	---	A	A	46	S
	* ID not provided by source

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CSPB_BACSU_001 *	F	17	L	CSPB_BACSU	---	---	B	F	17	L
2	UniProt	VAR_CSPB_BACSU_002 *	G	44	S	CSPB_BACSU	---	---	B	G	44	S
3	UniProt	VAR_CSPB_BACSU_003 *	A	46	S	CSPB_BACSU	---	---	B	A	46	S
	* ID not provided by source

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

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COLD_SHOCK	PS00352	'Cold-shock' domain signature.	CSPB_BACSU	15-33	2	A:15-33 B:15-33

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COLD_SHOCK	PS00352	'Cold-shock' domain signature.	CSPB_BACSU	15-33	1	A:15-33 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COLD_SHOCK	PS00352	'Cold-shock' domain signature.	CSPB_BACSU	15-33	1	- B:15-33

Exons (0, 0)

(no "Exon" information available for 3PF4)

Sequences/Alignments

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:66
 aligned with CSPB_BACSU | P32081 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACSU    1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKE 66
               SCOP domains d3pf4a_ A: Major cold shock protein                                SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeee......eeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------L--------------------------S-S-------------------- SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3pf4 A  1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKE 66
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with CSPB_BACSU | P32081 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACSU    1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKE 66
               SCOP domains d3pf4b_ B: Major cold shock protein                                SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeee......eeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------L--------------------------S-S-------------------- SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3pf4 B  1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKE 66
                                    10        20        30        40        50        60

Chain R from PDB  Type:RNA  Length:5
                                    
                  3pf4 R  1 UCUUU  5

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, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Cold shock DNA-binding domain-like (310)

Protein domain: Major cold shock protein (21)

Bacillus subtilis [TaxId: 1423] (10)

1a	d3pf4a_	A:
1b	d3pf4b_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 3PF4)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3PF4)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CSPB_BACSU | P32081)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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	Cis Peptide Bonds
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CSPB_BACSU \| P32081	:	1csp 1csq 1nmf 1nmg 2es2 2f52 2i5l 2i5m 3pf5

Related Entries Specified in the PDB File

1c9o	CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN BC-CSP
1csp	CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS MAJOR COLD SHOCK PROTEIN, CSPB: A UNIVERSAL NUCLEIC-ACID BINDING DOMAIN
2es2	CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS SUBTILIS COLD SHOCK PROTEIN BS-CSPB IN COMPLEX WITH HEXATHYMIDINE
2f52	SOLUTION STRUCTURE OF COLD SHOCK PROTEIN CSPB FROM BACILLUS SUBTILIS IN COMPLEX WITH HEPTATHYMIDINE
2hax	CRYSTAL STRUCTURE OF BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN IN COMPLEX WITH HEXATHYMIDINE