3FK2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RHOGAP DOMAIN OF HUMAN GLUCOCORTICOID RECEPTOR DNA-BINDING FACTOR 1

Authors :   L. Nedyalkova, Y. Tong, W. Tempel, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)

Date :   15 Dec 08 (Deposition) - 23 Dec 08 (Release) - 23 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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 :   Structural Genomics Consortium, Gtpase-Activating Protein, Sgc, Alternative Splicing, Anti-Oncogene, Cell Cycle, Cytoplasm, Dna-Binding, Gtpase Activation, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Signaling Protein, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Nedyalkova, Y. Tong, W. Tempel, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Rhogap Domain Of Human Glucocorticoid Receptor Dna-Binding Factor 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUCOCORTICOID RECEPTOR DNA-BINDING FACTOR 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21(DE3)-V2R-PRARE2
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 1212-1439
	Gene	:	GRLF1, GRF1, KIAA1722
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE AUTHORS SUSPECT THAT THE SAMPLE WAS TRUNCATED BY IN-SITU PROTEOLYSIS.
	Synonym	:	GLUCOCORTICOID RECEPTOR REPRESSION FACTOR 1, GRF- 1, RHO GAP P190A, P190-A

		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)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	UNX	8	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:1313	BINDING SITE FOR RESIDUE UNX A 1
2	AC2	SOFTWARE	THR B:1313	BINDING SITE FOR RESIDUE UNX B 2
3	AC3	SOFTWARE	THR C:1313	BINDING SITE FOR RESIDUE UNX C 3
4	AC4	SOFTWARE	THR D:1313	BINDING SITE FOR RESIDUE UNX D 4
5	AC5	SOFTWARE	GLN A:1431 , UNX C:7 , GLN C:1430 , GLN C:1431 , PRO C:1433 , PHE C:1434	BINDING SITE FOR RESIDUE UNX A 5
6	AC6	SOFTWARE	GLN B:1431 , UNX D:8 , GLN D:1431 , PRO D:1433 , PHE D:1434	BINDING SITE FOR RESIDUE UNX B 6
7	AC7	SOFTWARE	UNX A:5 , GLN A:1431 , PRO A:1433 , PHE A:1434 , GLN C:1431 , PHE C:1434	BINDING SITE FOR RESIDUE UNX C 7
8	AC8	SOFTWARE	UNX B:6 , GLN B:1431 , PRO B:1433 , PHE B:1434 , GLN D:1431	BINDING SITE FOR RESIDUE UNX D 8

(no "SS Bond" information available for 3FK2)

(no "Cis Peptide Bond" information available for 3FK2)

(no "SAP(SNP)/Variant" information available for 3FK2)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG35_HUMAN	1249-1436	4	A:1249-1436 B:1249-1436 C:1249-1436 D:1249-1436

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG35_HUMAN	1249-1436	1	A:1249-1436 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG35_HUMAN	1249-1436	1	- B:1249-1436 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG35_HUMAN	1249-1436	1	- - C:1249-1436 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHOGAP	PS50238	Rho GTPase-activating proteins domain profile.	RHG35_HUMAN	1249-1436	1	- - - D:1249-1436

(no "Exon" information available for 3FK2)

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:196
 aligned with RHG35_HUMAN | Q9NRY4 from UniProtKB/Swiss-Prot  Length:1499

    Alignment length:196
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      
         RHG35_HUMAN   1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFY 1437
               SCOP domains d3fk2a_ A: automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3fk2A00 A:1242-1437 GTPase -GAP domain                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RHOGAP  PDB: A:1249-1436 UniProt: 1249-1436                                                                                                                                                 - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fk2 A 1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFY 1437
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with RHG35_HUMAN | Q9NRY4 from UniProtKB/Swiss-Prot  Length:1499

    Alignment length:196
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      
         RHG35_HUMAN   1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFY 1437
               SCOP domains d3fk2b_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3fk2B00 B:1242-1437 GTPase -GAP domain                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RHOGAP  PDB: B:1249-1436 UniProt: 1249-1436                                                                                                                                                 - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fk2 B 1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPD---MDALTATRTYQTIIELFIQQCPFFFY 1437
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      |  -|     1421      1431      
                                                                                                                                                                                               1408   |                         
                                                                                                                                                                                                   1412

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with RHG35_HUMAN | Q9NRY4 from UniProtKB/Swiss-Prot  Length:1499

    Alignment length:195
                                  1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433     
         RHG35_HUMAN   1244 SNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFYN 1438
               SCOP domains d3fk2c_ C: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RHOGAP  PDB: C:1249-1436 UniProt: 1249-1436                                                                                                                                                 -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fk2 C 1244 SNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFYN 1438
                                  1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433

Chain D from PDB  Type:PROTEIN  Length:196
 aligned with RHG35_HUMAN | Q9NRY4 from UniProtKB/Swiss-Prot  Length:1499

    Alignment length:196
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      
         RHG35_HUMAN   1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFY 1437
               SCOP domains d3fk2d_ D: automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3fk2D00 D:1242-1437 GTPase -GAP domain                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh......hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RHOGAP  PDB: D:1249-1436 UniProt: 1249-1436                                                                                                                                                 - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fk2 D 1242 WESNYFGVPLTTVVTPEKPIPIFIERCIEYIEATGLSTEGIYRVSGNKSEMESLQRQFDQDHNLDLAEKDFTVNTVAGAMKSFFSELPDPLVPYNMQIDLVEAHKINDREQKLHALKEVLKKFPKENHEVFKYVISHLNKVSHNNKVNLMTSENLSICFWPTLMRPDFSTMDALTATRTYQTIIELFIQQCPFFFY 1437
                                  1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431

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 alpha proteins (14657)

Fold: GTPase activation domain, GAP (18)

Superfamily: GTPase activation domain, GAP (18)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3fk2a_	A:
1b	d3fk2c_	C:
1c	d3fk2d_	D:
1d	d3fk2b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Phosphatidylinositol 3-kinase; Chain A (12)

Homologous Superfamily: GTPase -GAP domain (12)

Human (Homo sapiens) (10)

1a	3fk2A00	A:1242-1437
1b	3fk2D00	D:1242-1437
1c	3fk2B00	B:1242-1437

(no "Pfam Domain" information available for 3FK2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RHG35_HUMAN | Q9NRY4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	GO:0001227	transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0030900	forebrain development	The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
	GO:0035024	negative regulation of Rho protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043116	negative regulation of vascular permeability	Any process that reduces the extent to which blood vessels can be pervaded by fluid.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	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:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

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(no "Related Entries Specified in the PDB File" available for 3FK2)

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