2IVX - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN CYCLIN T2 AT 1.8 A RESOLUTION (CASP TARGET)

Authors :   J. E. Debreczeni, A. N. Bullock, O. Fedorov, P. Savitsky, G. Berridge, S A. C. W. Pike, A. Turnbull, E. Ugochukwu, E. Papagrigoriou, F. Gorrec, M. Sundstrom, A. Edwards, C. Arrowsmith, J. Weigelt, F. Von Delft, S.

Date :   21 Jun 06 (Deposition) - 19 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Transcription Regulation, Cell Division, Phosphorylation, Nuclear Protein, Cyclin, Cell Cycle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Baumli, G. Lolli, E. D. Lowe, S. Troiani, L. Rusconi, A. N. Bullock, J. E. Debreczeni, S. Knapp, L. N. Johnson
The Structure Of P-Tefb (Cdk9/Cyclin T1), Its Complex With Flavopiridol And Regulation By Phosphorylation.
Embo J. V. 27 1907 2008
PubMed-ID: 18566585 | Reference-DOI: 10.1038/EMBOJ.2008.121

Molecule 1 - CYCLIN-T2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)R3
	Expression System Taxid	:	562
	Expression System Vector	:	PNIC28-BSA4
	Fragment	:	RESIDUES 7-263
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN CYCLIN T2, CYCT2

		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 (1, 6)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 2)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:201 , CYS A:204 , TRP A:209 , ILE A:211 , TRP A:220 , HOH A:2155	BINDING SITE FOR RESIDUE EDO A1263
2	AC2	SOFTWARE	ARG A:67 , GLU A:150 , CYS A:187 , PRO A:192 , HOH A:2001 , HOH A:2103 , HOH A:2156	BINDING SITE FOR RESIDUE EDO A1264
3	AC3	SOFTWARE	PHE A:74 , THR A:75 , LYS A:76 , ASN A:78	BINDING SITE FOR RESIDUE EDO A1265
4	AC4	SOFTWARE	LYS A:32 , CYS A:36 , PHE A:74 , THR A:75	BINDING SITE FOR RESIDUE EDO A1266
5	AC5	SOFTWARE	HIS B:201 , CYS B:204 , TRP B:209 , ILE B:211 , TRP B:220 , HOH B:2171	BINDING SITE FOR RESIDUE EDO B1264
6	AC6	SOFTWARE	CYS B:36 , THR B:75	BINDING SITE FOR RESIDUE EDO B1265

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

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

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

(no "PROSITE Motif" information available for 2IVX)

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000264157	1d	ENSE00001132542	chr2:135676395-135676582	188	CCNT2_HUMAN	1-53	53	2	A:7-53 B:9-53	47 45
1.2a	ENST00000264157	2a	ENSE00000827071	chr2:135677380-135677461	82	CCNT2_HUMAN	53-80	28	2	A:53-80 B:53-80	28 28
1.3	ENST00000264157	3	ENSE00001802057	chr2:135694411-135694539	129	CCNT2_HUMAN	81-123	43	2	A:81-123 B:81-123	43 43
1.4	ENST00000264157	4	ENSE00001792175	chr2:135696572-135696632	61	CCNT2_HUMAN	124-144	21	2	A:124-144 B:124-144	21 21
1.5a	ENST00000264157	5a	ENSE00000776509	chr2:135700182-135700244	63	CCNT2_HUMAN	144-165	22	2	A:144-165 B:144-165	22 22
1.7a	ENST00000264157	7a	ENSE00001596018	chr2:135703671-135703716	46	CCNT2_HUMAN	165-180	16	2	A:165-180 B:165-180	16 16
1.8b	ENST00000264157	8b	ENSE00001702605	chr2:135705306-135705469	164	CCNT2_HUMAN	180-235	56	2	A:180-235 B:180-235	56 56
1.9a	ENST00000264157	9a	ENSE00001792349	chr2:135710211-135710281	71	CCNT2_HUMAN	235-258	24	2	A:235-258 B:235-258	24 24
1.10e	ENST00000264157	10e	ENSE00001386482	chr2:135710800-135716912	6113	CCNT2_HUMAN	259-730	472	2	A:259-262 B:259-263	4 5

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:256
 aligned with CCNT2_HUMAN | O60583 from UniProtKB/Swiss-Prot  Length:730

    Alignment length:256
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256      
          CCNT2_HUMAN     7 ASSRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTQELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQA 262
               SCOP domains d2ivxa1 A:7-149 Cyclin-T2                                                                                                                      d2ivxa2 A:150-262 Cyclin-T2                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: A:7-53 UniProt: 1-53           ---------------------------Exon 1.3  PDB: A:81-123 UniProt: 81-123    Exon 1.4             --------------------Exon 1.7a       ------------------------------------------------------Exon 1.9a  PDB: A:235-251.10 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.2a  PDB: A:53-80     ---------------------------------------------------------------Exon 1.5a             --------------Exon 1.8b  PDB: A:180-235 UniProt: 180-235              --------------------------- Transcript 1 (2)
                 2ivx A   7 ASSRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQA 262
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with CCNT2_HUMAN | O60583 from UniProtKB/Swiss-Prot  Length:730

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
          CCNT2_HUMAN     9 SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTQELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQAA 263
               SCOP domains d2ivxb1 B:9-149 Cyclin-T2                                                                                                                    d2ivxb2 B:150-263 Cyclin-T2                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: B:9-53 UniProt: 1-53         ---------------------------Exon 1.3  PDB: B:81-123 UniProt: 81-123    Exon 1.4             --------------------Exon 1.7a       ------------------------------------------------------Exon 1.9a  PDB: B:235-251.10e Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.2a  PDB: B:53-80     ---------------------------------------------------------------Exon 1.5a             --------------Exon 1.8b  PDB: B:180-235 UniProt: 180-235              ---------------------------- Transcript 1 (2)
                 2ivx B   9 SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQAA 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

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: Cyclin-like (137)

Superfamily: Cyclin-like (137)

Family: Cyclin (117)

Protein domain: Cyclin-T2 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2ivxa1	A:7-149
1b	d2ivxa2	A:150-262
1c	d2ivxb1	B:9-149
1d	d2ivxb2	B:150-263

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

(no "Pfam Domain" information available for 2IVX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CCNT2_HUMAN | O60583)

molecular function
	GO:0097322	7SK snRNA binding	Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA).
	GO:0070063	RNA polymerase binding	Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0016538	cyclin-dependent protein serine/threonine kinase regulator activity	Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other 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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0001223	transcription coactivator binding	Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0019085	early viral transcription	The first phase of viral transcription that occurs after entry of the virus into the host cell, but prior to viral genome replication. It involves the transcription of genes for non-structural proteins, and for lytic viruses, the early gene products are involved in establishing control over the host cell.
	GO:0019086	late viral transcription	The transcription of the final group of viral genes of the viral life cycle, following middle transcription, or where middle transcription doesn't occur, following early transcription. Involves the transcription of genes encoding structural proteins.
	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that activates or increases the frequency, rate or extent of CDK activity.
	GO:1901409	positive regulation of phosphorylation of RNA polymerase II C-terminal domain	Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
	GO:0051147	regulation of muscle cell differentiation	Any process that modulates the frequency, rate or extent of muscle cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0008024	cyclin/CDK positive transcription elongation factor complex	A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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Description

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Ligands, Modified Residues, Ions (1, 6)

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