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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH CRA-19156

Authors :   J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Luong, A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands, E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari

Date :   13 May 04 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Histone Deacetylase, Zinc Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Luong, A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands, E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari
Structural Snapshots Of Human Hdac8 Provide Insights Into The Class I Histone Deacetylases
Structure V. 12 1325 2004
PubMed-ID: 15242608 | Reference-DOI: 10.1016/J.STR.2004.04.012
(for further references see the PDB file header)

Molecule 1 - HISTONE DEACETYLASE 8
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PFASTBACHTA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector	:	PSXB2
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	HDAC8, HDACL1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HDAC8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CRI	2	Ligand/Ion	5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLICACID 3-DIMETHYLAMIDE-4'-HYDROXYAMIDE
2	NA	2	Ligand/Ion	SODIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , CRI A:402	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , CRI B:402	BINDING SITE FOR RESIDUE ZN B 400
3	AC3	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200 , HIS B:201	BINDING SITE FOR RESIDUE NA B 401
4	AC4	SOFTWARE	LEU A:177 , ASP A:178 , LEU A:200 , TYR A:240 , THR A:268	BINDING SITE FOR RESIDUE NA A 401
5	AC5	SOFTWARE	HIS A:142 , HIS A:143 , PHE A:152 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , TYR A:306 , ZN A:400 , HOH A:478 , PHE B:152 , PRO B:273 , MET B:274 , TYR B:306 , CRI B:402	BINDING SITE FOR RESIDUE CRI A 402
6	AC6	SOFTWARE	PRO A:273 , CRI A:402 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , TYR B:306 , ZN B:400	BINDING SITE FOR RESIDUE CRI B 402

Asymmetric/Biological Unit

No.	Residues
1	A:244	-	A:287
2	B:244	-	B:287

Asymmetric/Biological Unit

No.	Residues
1	Gly A:341	-	Pro A:342
2	Phe B:208	-	Pro B:209
3	Gly B:341	-	Pro B:342

Asymmetric/Biological Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069140	H	180	R	HDAC8_HUMAN	Disease (CDLS5)	397515416	A/B	H	180	R
2	UniProt	VAR_069141	T	311	M	HDAC8_HUMAN	Disease (CDLS5)	397515417	A/B	T	311	M
3	UniProt	VAR_069142	G	320	R	HDAC8_HUMAN	Disease (CDLS5)	398122909	A/B	G	320	R
4	UniProt	VAR_069143	H	334	R	HDAC8_HUMAN	Disease (CDLS5)	397515418	A/B	H	334	R

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

(no "PROSITE Motif" information available for 1VKG)

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000373573	1a	ENSE00001889063	X:71792953-71792501	453	HDAC8_HUMAN	1-37	37	2	A:15-37 B:15-37	23 23
1.3a	ENST00000373573	3a	ENSE00001647366	X:71791959-71791907	53	HDAC8_HUMAN	38-55	18	2	A:38-55 B:38-55	18 18
1.4a	ENST00000373573	4a	ENSE00000978735	X:71788734-71788604	131	HDAC8_HUMAN	55-99	45	2	A:55-88 B:55-88	34 34
1.5a	ENST00000373573	5a	ENSE00001800363	X:71787880-71787739	142	HDAC8_HUMAN	99-146	48	2	A:104-146 B:104-146	43 43
1.6b	ENST00000373573	6b	ENSE00001682124	X:71715118-71715006	113	HDAC8_HUMAN	146-184	39	2	A:146-184 B:146-184	39 39
1.7b	ENST00000373573	7b	ENSE00001702232	X:71710856-71710779	78	HDAC8_HUMAN	184-210	27	2	A:184-210 B:184-210	27 27
1.9a	ENST00000373573	9a	ENSE00001682340	X:71708891-71708783	109	HDAC8_HUMAN	210-246	37	2	A:210-246 B:210-246	37 37
1.13b	ENST00000373573	13b	ENSE00001694695	X:71684581-71684409	173	HDAC8_HUMAN	246-304	59	2	A:246-304 B:246-304	59 59
1.15c	ENST00000373573	15c	ENSE00001436112	X:71681948-71681854	95	HDAC8_HUMAN	304-335	32	2	A:304-335 B:304-335	32 32
1.16b	ENST00000373573	16b	ENSE00001435962	X:71571688-71571583	106	HDAC8_HUMAN	336-371	36	2	A:336-371 B:336-371	36 36
1.18b	ENST00000373573	18b	ENSE00001859665	X:71549926-71549366	561	HDAC8_HUMAN	371-377	7	2	A:371-377 B:371-377	7 7

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
	(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:348
 aligned with HDAC8_HUMAN | Q9BY41 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:363
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
          HDAC8_HUMAN    15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
               SCOP domains d1vkga_ A: Histone deacetylase 8, HDAC8                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vkgA00 A:15-377  [code=3.40.800.20, no name defined]                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhh..---------------...hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhhh....eeeee.....hhhhhhhh.....eeeeeeee...............ee..ee..eeeeee....hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhh.................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------M--------R-------------R------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:15-37Exon 1.3a         -------------------------------------------Exon 1.5a  PDB: A:104-146 UniProt: 99-146       -------------------------------------Exon 1.7b  PDB: A:184-210  -----------------------------------Exon 1.13b  PDB: A:246-304 UniProt: 246-304                -------------------------------Exon 1.16b  PDB: A:336-371          ------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.4a  PDB: A:55-88 UniProt: 55-99       ----------------------------------------------Exon 1.6b  PDB: A:146-184              -------------------------Exon 1.9a  PDB: A:210-246            ---------------------------------------------------------Exon 1.15c  PDB: A:304-335      -----------------------------------1.18b   Transcript 1 (2)
                 1vkg A  15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDD---------------ATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    24        34        44        54        64        74        84   |     -       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
                                                                                                    88             104

Chain B from PDB  Type:PROTEIN  Length:348
 aligned with HDAC8_HUMAN | Q9BY41 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:363
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
          HDAC8_HUMAN    15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
               SCOP domains d1vkgb_ B: Histone deacetylase 8, HDAC8                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vkgB00 B:15-377  [code=3.40.800.20, no name defined]                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhh......hhhhhhhhhhhhh.hhhhheee.....hhhhhhh..hhhhhhhhhhhhhhh..---------------...hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee......hhhhhhhh....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhh............hhhhh................hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------M--------R-------------R------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:15-37Exon 1.3a         -------------------------------------------Exon 1.5a  PDB: B:104-146 UniProt: 99-146       -------------------------------------Exon 1.7b  PDB: B:184-210  -----------------------------------Exon 1.13b  PDB: B:246-304 UniProt: 246-304                -------------------------------Exon 1.16b  PDB: B:336-371          ------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.4a  PDB: B:55-88 UniProt: 55-99       ----------------------------------------------Exon 1.6b  PDB: B:146-184              -------------------------Exon 1.9a  PDB: B:210-246            ---------------------------------------------------------Exon 1.15c  PDB: B:304-335      -----------------------------------1.18b   Transcript 1 (2)
                 1vkg B  15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDD---------------ATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    24        34        44        54        64        74        84   |     -       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
                                                                                                    88             104

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Arginase/deacetylase (138)

Superfamily: Arginase/deacetylase (138)

Family: Histone deacetylase, HDAC (28)

Protein domain: Histone deacetylase 8, HDAC8 (5)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d1vkga_	A:
1b	d1vkgb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Arginase; Chain A (84)

Homologous Superfamily: [code=3.40.800.20, no name defined] (21)

Human (Homo sapiens) (17)

1a	1vkgA00	A:15-377
1b	1vkgB00	B:15-377

(no "Pfam Domain" information available for 1VKG)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HDAC8_HUMAN | Q9BY41)

molecular function
	GO:0030544	Hsp70 protein binding	Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
	GO:0051879	Hsp90 protein binding	Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
	GO:0032041	NAD-dependent histone deacetylase activity (H3-K14 specific)	Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.
	GO:0004407	histone deacetylase activity	Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0070932	histone H3 deacetylation	The modification of histone H3 by the removal of one or more acetyl groups.
	GO:0016575	histone deacetylation	The modification of histones by removal of acetyl groups.
	GO:0031397	negative regulation of protein ubiquitination	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	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:0071922	regulation of cohesin loading	Any process that modulates the frequency, rate or extent of a process in which a cohesin complex is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
	GO:0031647	regulation of protein stability	Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
	GO:0032204	regulation of telomere maintenance	Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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:0000118	histone deacetylase complex	A protein complex that possesses histone deacetylase activity.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:341 - Pro A:342	[ RasMol ]
		Gly B:341 - Pro B:342	[ RasMol ]
		Phe B:208 - Pro B:209	[ RasMol ]

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1t64	CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH TRICHOSTATIN A
1t67	CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH MS-344
1t69	CRYSTAL STRUCTURE OF HDAC8 COMPLEXED WITH SAHA

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

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Exons (11, 22)

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