2Q3G - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE PDZ DOMAIN OF HUMAN PDLIM7 BOUND TO A C-TERMINAL EXTENSION FROM HUMAN BETA-TROPOMYOSIN

Authors :   C. Gileadi, E. Papagrigoriou, J. Elkins, N. Burgess-Brown, E. Salah, O. Gileadi, C. Umeano, G. Bunkoczi, F. Von Delft, J. Uppenberg, A. C. W. Pike, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)

Date :   30 May 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.11

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

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

Reference :   C. Gileadi, E. Papagrigoriou, J. Elkins, N. Burgess-Brown, E. Salah, O. Gileadi, C. Umeano, G. Bunkoczi, F. Von Delft, J. Uppenberg, A. C. W. Pike, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, D. A. Doyle
Structure Of The Pdz Domain Of Human Pdlim7 Bound To A C-Terminal Extension From Human Beta-Tropomyosin
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PDZ AND LIM DOMAIN PROTEIN 7
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3) WITH WITH PRARE PLASMID ENCODING RARE CODON TRNAS,(CHLORAMPHENICOL- RESISTANT)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDLIM7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LIM MINERALIZATION PROTEIN, LMP, PROTEIN ENIGMA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:52 , ASP B:54 , GLY B:55 , SER B:78	BINDING SITE FOR RESIDUE CL B 601
2	AC2	SOFTWARE	PRO B:35 , GLY B:36 , ALA B:40 , GLN B:41	BINDING SITE FOR RESIDUE EDO B 1960
3	AC3	SOFTWARE	GLY A:43 , HOH A:3975 , HOH A:4058 , LYS B:69 , ALA B:72 , HOH B:2980 , HOH B:3079	BINDING SITE FOR RESIDUE EDO B 2960
4	AC4	SOFTWARE	LYS A:69 , ALA A:72 , HOH A:3978 , GLY B:43 , HOH B:2973 , HOH B:3064	BINDING SITE FOR RESIDUE EDO A 3960

(no "SS Bond" information available for 2Q3G)

Asymmetric Unit

No.	Residues
1	Gly A:10	-	Pro A:11
2	Ala A:12	-	Pro A:13
3	Gly B:10	-	Pro B:11
4	Ala B:12	-	Pro B:13

(no "SAP(SNP)/Variant" information available for 2Q3G)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PDLI7_HUMAN	9-85	2	A:9-84 B:9-84

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PDLI7_HUMAN	9-85	1	A:9-84 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PDLI7_HUMAN	9-85	1	- B:9-84

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000355841	1d	ENSE00001515758	chr5:176924584-176924529	56	PDLI7_HUMAN	-	0	0	-	-
1.2c	ENST00000355841	2c	ENSE00002200659	chr5:176923524-176923418	107	PDLI7_HUMAN	1-32	32	2	A:1-32 B:1-32	32 32
1.3b	ENST00000355841	3b	ENSE00001419643	chr5:176919678-176919527	152	PDLI7_HUMAN	33-83	51	2	A:33-83 B:33-83	51 51
1.4b	ENST00000355841	4b	ENSE00001400168	chr5:176919436-176919406	31	PDLI7_HUMAN	83-93	11	2	A:83-85 B:83-85	3 3
1.4g	ENST00000355841	4g	ENSE00001411967	chr5:176918926-176918808	119	PDLI7_HUMAN	94-133	40	2	A:86-88 B:86-88	3 3
1.5f	ENST00000355841	5f	ENSE00002167730	chr5:176918147-176918011	137	PDLI7_HUMAN	133-179	47	0	-	-
1.6	ENST00000355841	6	ENSE00001627630	chr5:176917907-176917871	37	PDLI7_HUMAN	179-191	13	0	-	-
1.7e	ENST00000355841	7e	ENSE00001774882	chr5:176916833-176916772	62	PDLI7_HUMAN	191-212	22	0	-	-
1.8	ENST00000355841	8	ENSE00001725106	chr5:176916628-176916394	235	PDLI7_HUMAN	212-290	79	0	-	-
1.9a	ENST00000355841	9a	ENSE00001748592	chr5:176915249-176915069	181	PDLI7_HUMAN	290-350	61	0	-	-
1.11b	ENST00000355841	11b	ENSE00001672261	chr5:176911191-176911071	121	PDLI7_HUMAN	351-391	41	0	-	-
1.12b	ENST00000355841	12b	ENSE00001766030	chr5:176910983-176910868	116	PDLI7_HUMAN	391-429	39	0	-	-
1.13d	ENST00000355841	13d	ENSE00001864426	chr5:176910731-176910397	335	PDLI7_HUMAN	430-457	28	0	-	-

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:89
 aligned with PDLI7_HUMAN | Q9NR12 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:113
                             1                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109   
          PDLI7_HUMAN     - -MDSFKVVLEGPAPWGFRLQGGKDFNVPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGSLTHIEAQNKIRACGERLSLGLSRAQPVQSKPQKASAPAADPPRYTFAPSVSL 112
               SCOP domains d2q3ga_ A: automated matches                                                                                      SCOP domains
               CATH domains 2q3gA00 A:0-88  [code=2.30.42.10, no name defined]                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeehhhheeeeeeee...hhhhhh......eeeee..ee.hhhhhhhhhhhhhh...eeeeeeeee.------------------------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDZ  PDB: A:9-84 UniProt: 9-85                                               --------------------------- PROSITE
           Transcript 1 (1) -Exon 1.2c  PDB: A:1-32          Exon 1.3b  PDB: A:33-83 UniProt: 33-83             ----------Exon 1.4g           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.4b  ------------------- Transcript 1 (2)
                 2q3g A   0 SMDSFKVVLEGPAPWGFRLQGGKDFNVPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGSLTHIEAQNKIRACGERLSLGLSRAI------------------------TSL  88
                                     9        19        29        39        49        59        69        79     |   -         -         -|  
                                                                                                                85                       86

Chain B from PDB  Type:PROTEIN  Length:88
 aligned with PDLI7_HUMAN | Q9NR12 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
          PDLI7_HUMAN     1 MDSFKVVLEGPAPWGFRLQGGKDFNVPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGSLTHIEAQNKIRACGERLSLGLSRAQPVQSKPQKASAPAADPPRYTFAPSVSL 112
               SCOP domains d2q3gb_ B: automated matches                                                                                     SCOP domains
               CATH domains 2q3gB00 B:1-88  [code=2.30.42.10, no name defined]                                                               CATH domains
           Pfam domains (1) --PDZ-2q3gB01 B:3-82                                                              ------------------------------ Pfam domains (1)
           Pfam domains (2) --PDZ-2q3gB02 B:3-82                                                              ------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeeeee......eeee.........eeeee...hhhhhh......eeeee..ee.hhhhhhhhhhhhhh...eeeeeeee..------------------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: B:9-84 UniProt: 9-85                                               --------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c  PDB: B:1-32          Exon 1.3b  PDB: B:33-83 UniProt: 33-83             ----------Exon 1.4g           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.4b  ------------------- Transcript 1 (2)
                 2q3g B   1 MDSFKVVLEGPAPWGFRLQGGKDFNVPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGSLTHIEAQNKIRACGERLSLGLSRAI------------------------TSL  88
                                    10        20        30        40        50        60        70        80    |    -         -        86  
                                                                                                               85                       86

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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d2q3ga_	A:
1b	d2q3gb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

Homologous Superfamily: [code=2.30.42.10, no name defined] (191)

Human (Homo sapiens) (120)

1a	2q3gA00	A:0-88
1b	2q3gB00	B:1-88

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2q3gB01	B:3-82
1b	PDZ-2q3gB02	B:3-82

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDLI7_HUMAN | Q9NR12)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	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: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.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
	GO:0001725	stress fiber	A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:12 - Pro A:13	[ RasMol ]
		Ala B:12 - Pro B:13	[ RasMol ]
		Gly A:10 - Pro A:11	[ RasMol ]
		Gly B:10 - Pro B:11	[ RasMol ]

Biological Units
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	2q3g
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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

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