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Title :   CRYSTAL STRUCTURE OF THE HUMAN CLP-36 (PDLIM1) BOUND TO THE C-TERMINAL PEPTIDE OF HUMAN ALPHA-ACTININ-1

Authors :   J. Uppenberg, C. Gileadi, J. Elkins, J. Bray, N. Burgess-Brown, E. Sala O. Gileadi, G. Bunkoczi, E. Ugochukwu, C. Umeano, F. Von Delft, J. Wei C. H. Arrowsmith, A. Edwards, M. Sundstrom, D. A. Doyle, Structural G Consortium (Sgc)

Date :   18 Apr 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Pdz Domain, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Uppenberg, C. Gileadi, J. Elkins, J. Bray, N. Burgess-Brown, E. Salah, O. Gileadi, G. Bunkoczi, E. Ugochukwu, C. Umeano, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, D. A. Doyle
The Crystal Structure Of The Human Clp-36 (Pdlim1) Bound To The C-Terminal Peptide Of Human Alpha-Actinin-1.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:54 , GLU A:56 , ASN A:76 , HOH A:214 , HOH A:237	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	ASP A:89 , ACT A:204 , HOH A:215	BINDING SITE FOR RESIDUE CA A 202
3	AC3	SOFTWARE	THR A:34	BINDING SITE FOR RESIDUE CL A 203
4	AC4	SOFTWARE	ARG A:17 , GLU A:87 , ASP A:89 , CA A:202 , HOH A:232	BINDING SITE FOR RESIDUE ACT A 204
5	AC5	SOFTWARE	LYS A:22 , GLU A:25 , GLN A:26 , PRO A:27 , LEU A:28 , VAL A:49 , ILE A:50 , THR A:58 , SER A:59 , HOH A:238	BINDING SITE FOR RESIDUE PG4 A 205
6	AC6	SOFTWARE	GLY A:12 , VAL A:33 , PRO A:35	BINDING SITE FOR RESIDUE PEG A 206

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000329399	1a	ENSE00001306547	chr10:97050781-97050577	205	PDLI1_HUMAN	1-32	32	1	A:1-32	32
1.3	ENST00000329399	3	ENSE00000986618	chr10:97031541-97031390	152	PDLI1_HUMAN	33-83	51	1	A:33-83	51
1.4	ENST00000329399	4	ENSE00000986619	chr10:97028619-97028535	85	PDLI1_HUMAN	83-111	29	1	A:83-90 (gaps)	10
1.5b	ENST00000329399	5b	ENSE00000716582	chr10:97023820-97023621	200	PDLI1_HUMAN	112-178	67	0	-	-
1.6b	ENST00000329399	6b	ENSE00000933030	chr10:97007123-97006972	152	PDLI1_HUMAN	178-229	52	0	-	-
1.7c	ENST00000329399	7c	ENSE00000933031	chr10:96998442-96998325	118	PDLI1_HUMAN	229-268	40	0	-	-
1.8c	ENST00000329399	8c	ENSE00001454795	chr10:96997868-96997329	540	PDLI1_HUMAN	268-329	62	0	-	-

Sequences/Alignments

Asymmetric/Biological 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:91
 aligned with PDLI1_HUMAN | O00151 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:93
                             1                                                                                           
                             |       9        19        29        39        49        59        69        79        89   
           PDLI1_HUMAN    - -MTTQQIDLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAALANLCIGDVITAIDGENTSNMTHLEAQNRIKGCTDNLTLTVARSEHKVWSPL 92
               SCOP domains d2pkta_ A: automated matches                                                                  SCOP domains
               CATH domains 2pktA00 A:0-90  [code=2.30.42.10, no name defined]                                            CATH domains
               Pfam domains ---PDZ-2pktA01 A:3-82                                                              ---------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeehhhheeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeeee...--... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:3-85 UniProt: 3-85                                                     ------- PROSITE
           Transcript 1 (1) -Exon 1.1a  PDB: A:1-32          Exon 1.3  PDB: A:33-83 UniProt: 33-83              --------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.4   Transcript 1 (2)
                  2pkt A  0 SMTTQQIDLQGPGPWGFRLVGGKDFEQPLAISRVTPGSKAALANLCIGDVITAIDGENTSNMTHLEAQNRIKGCTDNLTLTVARSEHE--SDL 90
                                     9        19        29        39        49        59        69        79       | -|  
                                                                                                                  87 88

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	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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDLI1_HUMAN | O00151)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	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.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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