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Title :   CRYSTAL STRUCTURE OF HUMAN LIM PROTEIN RIL (PDLIM4) PDZ DOMAIN BOUND TO THE C-TERMINAL PEPTIDE OF HUMAN ALPHA-ACTININ-1

Authors :   M. Soundararajan, L. Shrestha, A. C. W. Pike, E. Salah, N. Burgess-Brow J. Elkins, C. Umeano, E. Ugochukwu, F. Von Delft, C. H. Arrowsmith, A. J. Weigelt, M. Sundstrom, D. Doyle

Date :   30 May 07 (Deposition) - 12 Jun 07 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Actin, Stress, Fibre Dynamics, Cytoskeleton, Lim Domain, Metal-Binding, Phosphorylation, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Elkins, C. Gileadi, L. Shrestha, C. Phillips, J. Wang, J. R. C. Muniz, D. A. Doyle
Unusual Binding Interactions In Pdz Domain Crystal Structures Help Explain Binding Mechanisms.
Protein Sci. V. 19 731 2010
PubMed-ID: 20120020 | Reference-DOI: 10.1002/PRO.349

Molecule 1 - PDZ AND LIM DOMAIN PROTEIN 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Fragment	:	PDZ DOMAIN, RESIDUES 1-85
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PDLIM4, LIM PROTEIN RIL, REVERSION-INDUCED LIM PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	1PE	4	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:86 , HOH B:2001 , HOH B:2061 , HOH B:2065 , HOH B:2066 , HOH B:2069	BINDING SITE FOR RESIDUE MG B1090
2	AC2	SOFTWARE	ARG A:16 , ARG A:82 , ASP A:88 , HOH A:2072	BINDING SITE FOR RESIDUE EDO A1090
3	AC3	SOFTWARE	ALA B:25 , PRO B:26 , LEU B:27 , LEU B:48 , ILE B:49 , GLN B:50 , THR B:57 , GLU B:58 , HOH B:2043	BINDING SITE FOR RESIDUE 1PE B1091

(no "SS Bond" information available for 2V1W)

Asymmetric Unit

No.	Residues
1	Gly A:9	-	Pro A:10
2	Ser A:11	-	Pro A:12
3	Gly B:9	-	Pro B:10
4	Ser B:11	-	Pro B:12

(no "SAP(SNP)/Variant" information available for 2V1W)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PDLI4_HUMAN	8-84	2	A:8-84 B:8-84

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PDLI4_HUMAN	8-84	8	A:8-84 B:8-84

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000253754	1a	ENSE00001042731	chr5:131593364-131593520	157	PDLI4_HUMAN	1-31	31	2	A:1-31 B:1-31	31 31
1.3	ENST00000253754	3	ENSE00001713905	chr5:131598302-131598453	152	PDLI4_HUMAN	32-82	51	2	A:32-82 B:32-82	51 51
1.4a	ENST00000253754	4a	ENSE00000899290	chr5:131602157-131602238	82	PDLI4_HUMAN	82-109	28	2	A:82-89 (gaps) B:82-89 (gaps)	27 27
1.6a	ENST00000253754	6a	ENSE00000899292	chr5:131606608-131606786	179	PDLI4_HUMAN	110-169	60	0	-	-
1.6e	ENST00000253754	6e	ENSE00000899294	chr5:131606996-131607159	164	PDLI4_HUMAN	169-224	56	0	-	-
1.6h	ENST00000253754	6h	ENSE00000899296	chr5:131607484-131607601	118	PDLI4_HUMAN	224-263	40	0	-	-
1.7c	ENST00000253754	7c	ENSE00001909392	chr5:131607718-131609147	1430	PDLI4_HUMAN	263-330	68	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
	(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:89
 aligned with PDLI4_HUMAN | P50479 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
          PDLI4_HUMAN     1 MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEI 108
               SCOP domains d2v1wa_ A: automated matches                                                                                 SCOP domains
               CATH domains 2v1wA00 A:1-89  [code=2.30.42.10, no name defined]                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......eeeeeehhhheeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee....-------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:8-84 UniProt: 8-84                                               ------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-31         Exon 1.3  PDB: A:32-82 UniProt: 32-82              -------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.4a UniProt: 82-109   Transcript 1 (2)
                 2v1w A   1 MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEG-------------------ESDL  89
                                    10        20        30        40        50        60        70        80    |    -         -    |   
                                                                                                               85                  86

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with PDLI4_HUMAN | P50479 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:109
                             1                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99         
          PDLI4_HUMAN     - -MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEI 108
               SCOP domains d2v1wb_ B: automated matches                                                                                  SCOP domains
               CATH domains 2v1wB00 B:0-89  [code=2.30.42.10, no name defined]                                                            CATH domains
           Pfam domains (1) ----PDZ-2v1wB01 B:4-81                                                            --------------------------- Pfam domains (1)
           Pfam domains (2) ----PDZ-2v1wB02 B:4-81                                                            --------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee......eeeeeehhhheeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhh....eeeeeee....-------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: B:8-84 UniProt: 8-84                                               ------------------------ PROSITE
           Transcript 1 (1) -Exon 1.1a  PDB: B:1-31         Exon 1.3  PDB: B:32-82 UniProt: 32-82              -------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.4a UniProt: 82-109   Transcript 1 (2)
                 2v1w B   0 SMPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEG-------------------ESDL  89
                                     9        19        29        39        49        59        69        79     |   -         -     |   
                                                                                                                85                  86

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: 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	d2v1wa_	A:
1b	d2v1wb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	2v1wB00	B:0-89
1b	2v1wA00	A:1-89

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2v1wB01	B:4-81
1b	PDZ-2v1wB02	B:4-81

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDLI4_HUMAN | P50479)


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.

Asymmetric Unit
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	Cis Peptide Bonds
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		Gly B:9 - Pro B:10	[ RasMol ]
		Ser A:11 - Pro A:12	[ RasMol ]
		Ser B:11 - Pro B:12	[ RasMol ]

Biological Unit
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2v1x	CRYSTAL STRUCTURE OF HUMAN RECQ-LIKE DNA HELICASE

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