2VSP - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FOURTH PDZ DOMAIN OF PDZ DOMAIN-CONTAINING PROTEIN 1

Authors :   W. W. Yue, N. Shafqat, E. S. Pilka, C. Johansson, J. W. Murray, J. Elkins, A. Roos, C. Cooper, C. Phillips, E. Salah, F. Von Delft, D. Doyle, A. Edwards, M. Wikstrom, C. Arrowsmith, C. Bountra, U. Oppermann

Date :   28 Apr 08 (Deposition) - 03 Mar 09 (Release) - 03 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Pdz, Membrane, Cytoplasm, Phosphoprotein, Transport Protein, Casp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. W. Yue, N. Shafqat, E. S. Pilka, F. Von Delft, C. Johansson, J. Elkins, A. Roos, J. W. Murray, D. Doyle, A. Edwards, C. Arrowsmith, C. Bountra, U. Oppermann
Crystal Structure Of The Fourth Pdz Domain Of Pdz Domain-Containing Protein 1
To Be Published
PubMed: search

Molecule 1 - PDZ DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3-PRARE2
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FOURTH PDZ DOMAIN, RESIDUES 375-459
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MGC
	Synonym	:	CFTR-ASSOCIATED PROTEIN OF 70 KDA, NA/PI COTRANSPORTER C-TERMINAL-ASSOCIATED PROTEIN, NAPI-CAP1, NA+/H+ EXCHANGER REGULATORY FACTOR 3, SODIUM-HYDROGEN EXCHANGER REGULATORY FACTOR 3

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2VSP)

(no "Site" information available for 2VSP)

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_HUMAN	9-90 134-215 243-323 378-458	4	- - - A:378-456 B:378-455 C:378-456 D:378-456

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_HUMAN	9-90 134-215 243-323 378-458	1	- - - A:378-456 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_HUMAN	9-90 134-215 243-323 378-458	1	- - - - B:378-455 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_HUMAN	9-90 134-215 243-323 378-458	1	- - - - - C:378-456 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NHRF3_HUMAN	9-90 134-215 243-323 378-458	1	- - - - - - D:378-456

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000344770	3	ENSE00001411267	chr1:145743263-145743333	71	NHRF3_HUMAN	-	0	0	-	-
1.4b	ENST00000344770	4b	ENSE00001372163	chr1:145747042-145747253	212	NHRF3_HUMAN	1-70	70	0	-	-
1.5	ENST00000344770	5	ENSE00001759427	chr1:145748338-145748587	250	NHRF3_HUMAN	71-154	84	0	-	-
1.6	ENST00000344770	6	ENSE00001710717	chr1:145752428-145752564	137	NHRF3_HUMAN	154-199	46	0	-	-
1.7	ENST00000344770	7	ENSE00002188888	chr1:145753955-145754150	196	NHRF3_HUMAN	200-265	66	0	-	-
1.8	ENST00000344770	8	ENSE00001787521	chr1:145756417-145756613	197	NHRF3_HUMAN	265-330	66	0	-	-
1.9a	ENST00000344770	9a	ENSE00001784849	chr1:145761178-145761402	225	NHRF3_HUMAN	331-405	75	4	A:374-405 B:376-405 C:374-405 D:374-405	32 30 32 32
1.10a	ENST00000344770	10a	ENSE00001706980	chr1:145762039-145762329	291	NHRF3_HUMAN	406-502	97	4	A:406-456 B:406-455 C:406-456 D:406-456	51 50 51 51
1.12d	ENST00000344770	12d	ENSE00001365469	chr1:145763570-145764074	505	NHRF3_HUMAN	503-519	17	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:83
 aligned with NHRF3_HUMAN | Q5T2W1 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:83
                                   383       393       403       413       423       433       443       453   
          NHRF3_HUMAN   374 HKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
               SCOP domains d2vspa_ A: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...........................hhhhhh......eeeee..ee....hhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:378-456 UniProt: 378-458                                            PROSITE
               Transcript 1 Exon 1.9a  PDB: A:374-405       Exon 1.10a  PDB: A:406-456 UniProt: 406-502         Transcript 1
                 2vsp A 374 MKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
                                   383       393       403       413       423       433       443       453

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with NHRF3_HUMAN | Q5T2W1 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:80
                                   385       395       405       415       425       435       445       455
          NHRF3_HUMAN   376 PKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVC 455
               SCOP domains d2vspb_ B: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeee..eeeeee......hhhhhh......eeeee..ee....hhhhhhhhhhh....eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: B:378-455 UniProt: 378-458                                           PROSITE
               Transcript 1 Exon 1.9a  PDB: B:376-405     Exon 1.10a  PDB: B:406-455 UniProt: 406-502        Transcript 1
                 2vsp B 376 PKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVC 455
                                   385       395       405       415       425       435       445       455

Chain C from PDB  Type:PROTEIN  Length:83
 aligned with NHRF3_HUMAN | Q5T2W1 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:83
                                   383       393       403       413       423       433       443       453   
          NHRF3_HUMAN   374 HKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
               SCOP domains d2vspc_ C: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........eee......eee......hhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: C:378-456 UniProt: 378-458                                            PROSITE
               Transcript 1 Exon 1.9a  PDB: C:374-405       Exon 1.10a  PDB: C:406-456 UniProt: 406-502         Transcript 1
                 2vsp C 374 MKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
                                   383       393       403       413       423       433       443       453

Chain D from PDB  Type:PROTEIN  Length:83
 aligned with NHRF3_HUMAN | Q5T2W1 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:83
                                   383       393       403       413       423       433       443       453   
          NHRF3_HUMAN   374 HKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
               SCOP domains d2vspd_ D: automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----PDZ-2vspD01 D:378-455                                                         - Pfam domains (1)
           Pfam domains (2) ----PDZ-2vspD02 D:378-455                                                         - Pfam domains (2)
           Pfam domains (3) ----PDZ-2vspD03 D:378-455                                                         - Pfam domains (3)
           Pfam domains (4) ----PDZ-2vspD04 D:378-455                                                         - Pfam domains (4)
         Sec.struct. author ..eeeeeee.........eee......eee......hhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: D:378-456 UniProt: 378-458                                            PROSITE
               Transcript 1 Exon 1.9a  PDB: D:374-405       Exon 1.10a  PDB: D:406-456 UniProt: 406-502         Transcript 1
                 2vsp D 374 MKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCG 456
                                   383       393       403       413       423       433       443       453

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

)

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	d2vspa_	A:
1b	d2vspb_	B:
1c	d2vspc_	C:
1d	d2vspd_	D:

(no "CATH Domain" information available for 2VSP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2vspD01	D:378-455
1b	PDZ-2vspD02	D:378-455
1c	PDZ-2vspD03	D:378-455
1d	PDZ-2vspD04	D:378-455

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NHRF3_HUMAN | Q5T2W1)

molecular function
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005124	scavenger receptor binding	Interacting selectively and non-covalently with scavenger receptors, a family of proteins that are expressed on myeloid cells and are involved in the uptake of effete cellular components and foreign particles.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0015879	carnitine transport	The directed movement of carnitine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0015893	drug transport	The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0034767	positive regulation of ion transmembrane transport	Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0090314	positive regulation of protein targeting to membrane	Any process that increases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0044070	regulation of anion transport	Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0031526	brush border membrane	The portion of the plasma membrane surrounding the brush border.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0031528	microvillus membrane	The portion of the plasma membrane surrounding a microvillus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	2vsp
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	NHRF3_HUMAN \| Q5T2W1	:	2eei 2eej 3tmh 4q2p

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