3KZD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FREE T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ DOMAIN

Authors :   T. R. Shepherd, E. J. Fuentes

Date :   08 Dec 09 (Deposition) - 21 Apr 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Pdz, Cell Junction, Cell Adhesion, Signaling Protein, Tiam1, Guanine Nucleotide Exchange Factor, Guanine-Nucleotide Releasing Factor, Lipoprotein, Myristate, Phosphoprotein, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. R. Shepherd, S. M. Klaus, X. Liu, S. Ramaswamy, K. A. Demali, E. J. Fuentes
The Tiam1 Pdz Domain Couples To Syndecan1 And Promotes Cell-Matrix Adhesion.
J. Mol. Biol. V. 398 730 2010
PubMed-ID: 20361982 | Reference-DOI: 10.1016/J.JMB.2010.03.047

Molecule 1 - T-LYMPHOMA INVASION AND METASTASIS-INDUCING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A-6HIS-RTEV
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN
	Gene	:	TIAM1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TIAM-1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3KZD)

(no "Site" information available for 3KZD)

(no "SS Bond" information available for 3KZD)

(no "Cis Peptide Bond" information available for 3KZD)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051993	Q	844	H	TIAM1_HUMAN	Polymorphism	16987932	A	H	844	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	TIAM1_HUMAN	845-908	1	A:845-908

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000286827	2	ENSE00001372551	chr21:32931290-32931240	51	TIAM1_HUMAN	-	0	0	-	-
1.3	ENST00000286827	3	ENSE00001367893	chr21:32836348-32836296	53	TIAM1_HUMAN	-	0	0	-	-
1.5	ENST00000286827	5	ENSE00001383160	chr21:32711737-32711558	180	TIAM1_HUMAN	-	0	0	-	-
1.6	ENST00000286827	6	ENSE00001365575	chr21:32649224-32649048	177	TIAM1_HUMAN	-	0	0	-	-
1.7b	ENST00000286827	7b	ENSE00001025653	chr21:32639299-32638326	974	TIAM1_HUMAN	1-321	321	0	-	-
1.8	ENST00000286827	8	ENSE00001025652	chr21:32624505-32624058	448	TIAM1_HUMAN	322-471	150	0	-	-
1.9	ENST00000286827	9	ENSE00001025654	chr21:32617976-32617804	173	TIAM1_HUMAN	471-528	58	0	-	-
1.10	ENST00000286827	10	ENSE00001025660	chr21:32598266-32598042	225	TIAM1_HUMAN	529-603	75	0	-	-
1.11	ENST00000286827	11	ENSE00001025647	chr21:32595907-32595722	186	TIAM1_HUMAN	604-665	62	0	-	-
1.12	ENST00000286827	12	ENSE00001025659	chr21:32590015-32589869	147	TIAM1_HUMAN	666-714	49	0	-	-
1.13a	ENST00000286827	13a	ENSE00001265070	chr21:32585788-32585714	75	TIAM1_HUMAN	715-739	25	0	-	-
1.14	ENST00000286827	14	ENSE00001025641	chr21:32582531-32582361	171	TIAM1_HUMAN	740-796	57	0	-	-
1.15	ENST00000286827	15	ENSE00001025658	chr21:32575328-32575224	105	TIAM1_HUMAN	797-831	35	0	-	-
1.16	ENST00000286827	16	ENSE00001025636	chr21:32567621-32567540	82	TIAM1_HUMAN	832-859	28	1	A:840-859 (gaps)	20
1.17	ENST00000286827	17	ENSE00001025648	chr21:32559403-32559317	87	TIAM1_HUMAN	859-888	30	1	A:859-888	30
1.18	ENST00000286827	18	ENSE00001025649	chr21:32554962-32554738	225	TIAM1_HUMAN	888-963	76	1	A:888-930	43
1.19	ENST00000286827	19	ENSE00001025650	chr21:32537382-32537279	104	TIAM1_HUMAN	963-997	35	0	-	-
1.20	ENST00000286827	20	ENSE00001025643	chr21:32526744-32526565	180	TIAM1_HUMAN	998-1057	60	0	-	-
1.21	ENST00000286827	21	ENSE00001025638	chr21:32525452-32525384	69	TIAM1_HUMAN	1058-1080	23	0	-	-
1.22	ENST00000286827	22	ENSE00001025637	chr21:32525079-32524954	126	TIAM1_HUMAN	1081-1122	42	0	-	-
1.23b	ENST00000286827	23b	ENSE00001025651	chr21:32519321-32519213	109	TIAM1_HUMAN	1123-1159	37	0	-	-
1.24	ENST00000286827	24	ENSE00001610053	chr21:32513822-32513643	180	TIAM1_HUMAN	1159-1219	61	0	-	-
1.25	ENST00000286827	25	ENSE00001722006	chr21:32513554-32513436	119	TIAM1_HUMAN	1219-1258	40	0	-	-
1.26	ENST00000286827	26	ENSE00001700177	chr21:32508359-32508251	109	TIAM1_HUMAN	1259-1295	37	0	-	-
1.27	ENST00000286827	27	ENSE00001806004	chr21:32503266-32503208	59	TIAM1_HUMAN	1295-1314	20	0	-	-
1.28a	ENST00000286827	28a	ENSE00001667545	chr21:32502633-32502531	103	TIAM1_HUMAN	1315-1349	35	0	-	-
1.29	ENST00000286827	29	ENSE00001597652	chr21:32499470-32499383	88	TIAM1_HUMAN	1349-1378	30	0	-	-
1.30a	ENST00000286827	30a	ENSE00001769773	chr21:32497012-32496840	173	TIAM1_HUMAN	1378-1436	59	0	-	-
1.31b	ENST00000286827	31b	ENSE00001612577	chr21:32493155-32490734	2422	TIAM1_HUMAN	1436-1591	156	0	-	-

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:85
 aligned with TIAM1_HUMAN | Q13009 from UniProtKB/Swiss-Prot  Length:1591

    Alignment length:91
                                   849       859       869       879       889       899       909       919       929 
          TIAM1_HUMAN   840 PKVTQSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMLKDFLSQPSLGLLVRTYPEL 930
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----PDZ-3k      zdA01 A:845-925                                                      ----- Pfam domains
         Sec.struct. author ..eeeeeeee.------...eeeeee......eeeeeee...hhhhhh......eeeee..ee.hhhhhhhhhhhhhh.eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----H-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:845-908 UniProt: 845-908                            ---------------------- PROSITE
           Transcript 1 (1) Exon 1.16           ----------------------------Exon 1.18  PDB: A:888-930 UniProt: 888-963  Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.17  PDB: A:859-888     ------------------------------------------ Transcript 1 (2)
                 3kzd A 840 GKVTHSIHIEK------TYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEILEINNRAADALNSSMLKDFLSQPSLGLLVRTYPEL 930
                                   849|      859       869       879       889       899       909       919       929 
                                    850    857

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 '\|'

(no "SCOP Domain" information available for 3KZD)

(no "CATH Domain" information available for 3KZD)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

PDZ-3kzdA01

A:845-925

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TIAM1_HUMAN | Q13009)

molecular function
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0030676	Rac guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0017016	Ras GTPase binding	Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0030971	receptor tyrosine kinase binding	Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
	GO:0005057	signal transducer activity, downstream of receptor	Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
biological process
	GO:0016601	Rac protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state.
	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
	GO:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0003300	cardiac muscle hypertrophy	The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:1990138	neuron projection extension	Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0043507	positive regulation of JUN kinase activity	Any process that activates or increases the frequency, rate or extent of JUN kinase activity.
	GO:1904268	positive regulation of Schwann cell chemotaxis	Any process that activates or increases the frequency, rate or extent of Schwann cell chemotaxis.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0061003	positive regulation of dendritic spine morphogenesis	Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:0072657	protein localization to membrane	A process in which a protein is transported to, or maintained in, a specific location in a membrane.
	GO:0070372	regulation of ERK1 and ERK2 cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:1904338	regulation of dopaminergic neuron differentiation	Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation.
	GO:0061178	regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:2000050	regulation of non-canonical Wnt signaling pathway	Any process that modulates the frequency, rate or extent of non-canonical Wnt signaling pathway.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
	GO:0042220	response to cocaine	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 cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0044295	axonal growth cone	The migrating motile tip of a growing nerve cell axon.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0044291	cell-cell contact zone	Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0044304	main axon	The main axonal trunk, as opposed to the collaterals; i.e., excluding collaterals, terminal, spines, or dendrites.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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: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.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.
	GO:0036477	somatodendritic compartment	The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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	TIAM1_HUMAN \| Q13009	:	2d8i 3kze 4gvc 4gvd 4k2o 4k2p 4nxp 4nxq 4nxr

3kze	CRYSTAL STRUCTURE OF T-CELL LYMPHOMA INVASION AND METASTASIS-1 PDZ IN COMPLEX WITH SSRKEYYA PEPTIDE

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