1ZTG | PD0675 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HUMAN ALPHA POLYC BINDING PROTEIN KH1

Authors :   M. Sidiqi, J. A. Wilce, A. Barker, J. Schmidgerger, P. J. Leedman, M. C. J

Date :   27 May 05 (Deposition) - 27 May 06 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D,Y,Z
Biol. Unit 1: A,D,Y  (1x)
Biol. Unit 2: B,C,Z  (1x)

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

Reference :   Y. M. K. Yoga, D. A. K. Traore, M. Sidiqi, C. Szeto, N. R. Pendini, A. Barker, P. J. Leedman, J. A. Wilce, M. C. J. Wilce
Contribution Of The First K-Homology Domain Of Poly(C)-Binding Protein 1 To Its Affinity And Specificity For C-Rich Oligonucleotides
Nucleic Acids Res. V. 40 5101 2012
PubMed-ID: 22344691 | Reference-DOI: 10.1093/NAR/GKS058

Molecule 1 - POLY(RC)-BINDING PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P2
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	KH1
	Gene	:	PCBP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PCBP1, ALPHA-CP1, HNRNP-E1, NUCLEIC ACID BINDING PROTEIN SUB2.3

*Molecule 2 - 5'-D(PCPCPCPTPCPCPCPT)-3'*
	Chains	:	Y, Z
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	Y	Z
Biological Unit 1 (1x)	:	A			D	Y
Biological Unit 2 (1x)	:		B	C			Z

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZTG)

(no "Site" information available for 1ZTG)

Asymmetric Unit

No.	Residues
1	A:54	-	B:54
2	C:54	-	D:54

Asymmetric Unit

No.	Residues
1	Ile A:83	-	Asn A:84
2	Gly B:12	-	Ile B:13
3	Asp D:82	-	Ile D:83

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PCBP1_HUMAN	13-75 97-162 279-343	4	A:14-75 B:14-75 C:14-75 D:14-75 - -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PCBP1_HUMAN	13-75 97-162 279-343	2	A:14-75 - - D:14-75 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PCBP1_HUMAN	13-75 97-162 279-343	2	- B:14-75 C:14-75 - - -

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000303577	1	ENSE00001129885	chr2:70314585-70316332	1748	PCBP1_HUMAN	1-453	453	4	A:13-84 B:12-85 (gaps) C:12-83 (gaps) D:13-83	72 82 80 71

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
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Chain A from PDB  Type:PROTEIN  Length:72
 aligned with PCBP1_HUMAN | Q15365 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:72
                                    22        32        42        52        62        72        82  
           PCBP1_HUMAN   13 TLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDIN 84
               SCOP domains d1ztga_ A: automated matches                                             SCOP domains
               CATH domains 1ztgA00 A:13-84  [code=3.30.1370.10, no name defined]                    CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhhh...hhhhhhhhhhhh.eeee......eeeeeeeehhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE KH_TYPE_1  PDB: A:14-75 UniProt: 13-75                         --------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:13-84 UniProt: 1-453 [INCOMPLETE]                       Transcript 1
                  1ztg A 13 ILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDIN 84
                                    22        32        42        52        62        72        82

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with PCBP1_HUMAN | Q15365 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:82
                                    13        23        33        43        53        63        73        83  
           PCBP1_HUMAN    4 GVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDINS 85
               SCOP domains d1        ztgb_ B: automated matches                                               SCOP domains
               CATH domains 1z        tgB00 B:12-85  [code=3.30.1370.10, no name defined]                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------eeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee......eeeeeeeehhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------KH_TYPE_1  PDB: B:14-75 UniProt: 13-75                         ---------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:12-85 (gaps) UniProt: 1-453 [INCOMPLETE]                          Transcript 1
                  1ztg B 12 GI--------LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDINS 85
                             |       -|       23        33        43        53        63        73        83  
                            13       14

Chain C from PDB  Type:PROTEIN  Length:72
 aligned with PCBP1_HUMAN | Q15365 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:80
                                    13        23        33        43        53        63        73        83
           PCBP1_HUMAN    4 GVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDI 83
               SCOP domains d1        ztgc_ C: automated matches                                             SCOP domains
               CATH domains 1z        tgC00 C:12-83  [code=3.30.1370.10, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------eeeeeeee.hhhhhhh...hhhhhhhhhhhh.eeee......eeeeeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------KH_TYPE_1  PDB: C:14-75 UniProt: 13-75                         -------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:12-83 (gaps) UniProt: 1-453 [INCOMPLETE]                        Transcript 1
                  1ztg C 12 GI--------LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDI 83
                             |       -|       23        33        43        53        63        73        83
                            13       14

Chain D from PDB  Type:PROTEIN  Length:71
 aligned with PCBP1_HUMAN | Q15365 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:71
                                    22        32        42        52        62        72        82 
           PCBP1_HUMAN   13 TLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDI 83
               SCOP domains d1ztgd_ D: automated matches                                            SCOP domains
               CATH domains 1ztgD00 D:13-83  [code=3.30.1370.10, no name defined]                   CATH domains
           Pfam domains (1) --KH_1-1ztgD01 D:15-75                                         -------- Pfam domains (1)
           Pfam domains (2) --KH_1-1ztgD02 D:15-75                                         -------- Pfam domains (2)
           Pfam domains (3) --KH_1-1ztgD03 D:15-75                                         -------- Pfam domains (3)
           Pfam domains (4) --KH_1-1ztgD04 D:15-75                                         -------- Pfam domains (4)
         Sec.struct. author .eeeeeeeehhhhhhhh...hhhhhhhhhhhh.eeee......eeeeeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE KH_TYPE_1  PDB: D:14-75 UniProt: 13-75                         -------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:13-83 UniProt: 1-453 [INCOMPLETE]                      Transcript 1
                  1ztg D 13 ILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKLEEDI 83
                                    22        32        42        52        62        72        82

Chain Y from PDB  Type:DNA  Length:8
                                       
                  1ztg Y  3 CCCTCCCT 10

Chain Z from PDB  Type:DNA  Length:8
                                       
                  1ztg Z  3 CCCTCCCT 10

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: Alpha and beta proteins (a+b) (23004)

Fold: Eukaryotic type KH-domain (KH-domain type I) (51)

Superfamily: Eukaryotic type KH-domain (KH-domain type I) (51)

Family: Eukaryotic type KH-domain (KH-domain type I) (40)

Protein domain: automated matches (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d1ztga_	A:
1b	d1ztgd_	D:
1c	d1ztgb_	B:
1d	d1ztgc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein S8; Chain: A, domain 1 (139)

Homologous Superfamily: [code=3.30.1370.10, no name defined] (23)

Human (Homo sapiens) (13)

1a	1ztgB00	B:12-85
1b	1ztgA00	A:13-84
1c	1ztgC00	C:12-83
1d	1ztgD00	D:13-83

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: KH (43)

Family: KH_1 (21)

Homo sapiens (Human) (17)

1a	KH_1-1ztgD01	D:15-75
1b	KH_1-1ztgD02	D:15-75
1c	KH_1-1ztgD03	D:15-75
1d	KH_1-1ztgD04	D:15-75

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PCBP1_HUMAN | Q15365)

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:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0010467	gene expression	The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ztg)

	Sites
(no "Sites" information available for 1ztg)

	Cis Peptide Bonds
		Asp D:82 - Ile D:83	[ RasMol ]
		Gly B:12 - Ile B:13	[ RasMol ]
		Ile A:83 - Asn A:84	[ RasMol ]

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	1ztg
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	PCBP1_HUMAN \| Q15365
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	PCBP1_HUMAN \| Q15365	:	1wvn 3vke

(no "Related Entries Specified in the PDB File" available for 1ZTG)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (1, 4)

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