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Title :   CRYSTAL STRUCTURE OF KH1 DOMAIN OF HUMAN PCBP2 COMPLEXED TO SINGLE-STRANDED 12-MER TELOMERIC DNA

Authors :   T. L. James, J. Lee

Date :   02 May 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

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

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

Reference :   Z. Du, J. K. Lee, S. Fenn, R. Tjhen, R. M. Stroud, T. L. James
X-Ray Crystallographic And Nmr Studies Of Protein-Protein And Protein-Nucleic Acid Interactions Involving The Kh Domains From Human Poly(C)-Binding Protein-2.
Rna V. 13 1043 2007
PubMed-ID: 17526645 | Reference-DOI: 10.1261/RNA.410107

Molecule 1 - 12-MER C-RICH STRAND OF HUMAN TELOMERIC DNA
	Chains	:	E, G
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - POLY(RC)-BINDING PROTEIN 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FIRST KH DOMAIN OF HUMAN POLY(C)-BINDING PROTEIN
	Gene	:	PCBP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALPHA-CP2, HNRNP-E2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2PQU)

(no "SS Bond" information available for 2PQU)

(no "Cis Peptide Bond" information available for 2PQU)

(no "SAP(SNP)/Variant" information available for 2PQU)

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.	PCBP2_HUMAN	13-75 97-162 287-351	4	A:13-75 B:13-75 C:13-75 D:13-75 - -

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.	PCBP2_HUMAN	13-75 97-162 287-351	2	A:13-75 B:13-75 - - - -

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.	PCBP2_HUMAN	13-75 97-162 287-351	2	- - C:13-75 D:13-75 - -

(no "Exon" information available for 2PQU)

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:72
 aligned with PCBP2_HUMAN | Q15366 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:72
                                    19        29        39        49        59        69        79  
          PCBP2_HUMAN    10 LNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE  81
               SCOP domains d2pqua_ A: Poly(RC)-binding protein 2                                    SCOP domains
               CATH domains 2pquA00 A:10-81  [code=3.30.1370.10, no name defined]                    CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee......eeeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---KH_TYPE_1  PDB: A:13-75 UniProt: 13-75                         ------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2pqu A  10 KNVTLTIRLLmHGKEVGSIIGKKGESVKKmREESGARINISEGNCPERIITLAGPTNAIFKAFAmIIDKLEE  81
                                    19|       29        39        49        59        69    |   79  
                                     20-MSE             39-MSE                             74-MSE

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with PCBP2_HUMAN | Q15366 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:70
                                    21        31        41        51        61        71        81
          PCBP2_HUMAN    12 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE  81
               SCOP domains d2pqub_ B: Poly(RC)-binding protein 2                                  SCOP domains
               CATH domains 2pquB00 B:12-81  [code=3.30.1370.10, no name defined]                  CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeee.......eeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: B:13-75 UniProt: 13-75                         ------ PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2pqu B  12 VTLTIRLLmHGKEVGSIIGKKGESVKKmREESGARINISEGNCPERIITLAGPTNAIFKAFAmIIDKLEE  81
                                    21        31       |41        51        61        71  |     81
                                   20-MSE             39-MSE                             74-MSE

Chain C from PDB  Type:PROTEIN  Length:70
 aligned with PCBP2_HUMAN | Q15366 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:70
                                    21        31        41        51        61        71        81
          PCBP2_HUMAN    12 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE  81
               SCOP domains d2pquc_ C: Poly(RC)-binding protein 2                                  SCOP domains
               CATH domains 2pquC00 C:12-81  [code=3.30.1370.10, no name defined]                  CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee......eeeeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: C:13-75 UniProt: 13-75                         ------ PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2pqu C  12 VTLTIRLLmHGKEVGSIIGKKGESVKKmREESGARINISEGNCPERIITLAGPTNAIFKAFAmIIDKLEE  81
                                    21        31       |41        51        61        71  |     81
                                   20-MSE             39-MSE                             74-MSE

Chain D from PDB  Type:PROTEIN  Length:70
 aligned with PCBP2_HUMAN | Q15366 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:70
                                    21        31        41        51        61        71        81
          PCBP2_HUMAN    12 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE  81
               SCOP domains d2pqud_ D: Poly(RC)-binding protein 2                                  SCOP domains
               CATH domains 2pquD00 D:12-81  [code=3.30.1370.10, no name defined]                  CATH domains
           Pfam domains (1) ---KH_1-2pquD01 D:15-75                                         ------ Pfam domains (1)
           Pfam domains (2) ---KH_1-2pquD02 D:15-75                                         ------ Pfam domains (2)
           Pfam domains (3) ---KH_1-2pquD03 D:15-75                                         ------ Pfam domains (3)
           Pfam domains (4) ---KH_1-2pquD04 D:15-75                                         ------ Pfam domains (4)
         Sec.struct. author ..eeeeeeeehhhhhhhhh..hhhhhhhhhhhh.eeee......eeeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -KH_TYPE_1  PDB: D:13-75 UniProt: 13-75                         ------ PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2pqu D  12 VTLTIRLLmHGKEVGSIIGKKGESVKKmREESGARINISEGNCPERIITLAGPTNAIFKAFAmIIDKLEE  81
                                    21        31       |41        51        61        71  |     81
                                   20-MSE             39-MSE                             74-MSE

Chain E from PDB  Type:DNA  Length:12
                                            
                 2pqu E 498 AACCCTAACCCT 509
                                   507

Chain G from PDB  Type:DNA  Length:12
                                            
                 2pqu G 499 AACCCTAACCCT 510
                                   508

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( (-)

)

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: Poly(RC)-binding protein 2 (4)

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

1a	d2pqua_	A:
1b	d2pqub_	B:
1c	d2pquc_	C:
1d	d2pqud_	D:

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)

[unclassified] (8)

1a	2pquA00	A:10-81
1b	2pquB00	B:12-81
1c	2pquC00	C:12-81
1d	2pquD00	D:12-81

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: KH (43)

Family: KH_1 (21)

Homo sapiens (Human) (17)

1a	KH_1-2pquD01	D:15-75
1b	KH_1-2pquD02	D:15-75
1c	KH_1-2pquD03	D:15-75
1d	KH_1-2pquD04	D:15-75

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PCBP2_HUMAN | Q15366)

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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0075522	IRES-dependent viral translational initiation	Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	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:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0016071	mRNA metabolic process	The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
	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:0050687	negative regulation of defense response to virus	Any process that stops, prevents or reduces the rate or extent of antiviral mechanisms, thereby facilitating viral replication.
	GO:0032480	negative regulation of type I interferon production	Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	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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	PCBP2_HUMAN \| Q15366	:	2axy 2jzx 2p2r 2py9

2axy	THE SAME PROTEIN COMPLEXED WITH 7-MER TELOMERIC DNA

Description

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