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Title :   CRYSTAL STRUCTURE OF SGF29 IN COMPLEX WITH H3K4ME3 PEPTIDE

Authors :   C. Bian, W. Tempel, C. Xu, Y. Guo, A. Dong, L. Crombet, C. Bountra, J. Weig C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)

Date :   31 Mar 10 (Deposition) - 28 Apr 10 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.37

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

Keywords :   Structural Genomics Consortium, Sgc, Nucleus, Transcription, Transcription Regulation, Chromosomal Protein, Dna-Binding, Nucleosome Core (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Bian, C. Xu, J. Ruan, K. K. Lee, T. L. Burke, W. Tempel, D. Barsyte, J. Li, M. Wu, B. O. Zhou, B. E. Fleharty, A. Paulson, A. Allali-Hassani, J. Q. Zhou, G. Mer, P. A. Grant, J. L. Workman, J. Zang, J. Min
Sgf29 Binds Histone H3K4Me2/3 And Is Required For Saga Complex Recruitment And Histone H3 Acetylation.
Embo J. V. 30 2829 2011
PubMed-ID: 21685874 | Reference-DOI: 10.1038/EMBOJ.2011.193

Molecule 1 - SAGA-ASSOCIATED FACTOR 29 HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21(DE3)-V2R-PRARE2
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 115-293
	Gene	:	CCDC101, SGF29
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	COILED-COIL DOMAIN-CONTAINING PROTEIN 101

Molecule 2 - HISTONE H3
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 2-9
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Other Details	:	H3K4ME3 8MER
	Synonym	:	H3K4ME3 8MER
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 20)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	2	Ligand/Ion	SULFATE ION
5	UNX	11	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (5, 10)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION
5	UNX	5	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION
5	UNX	6	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 3 (5, 10)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION
5	UNX	5	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:48 , GLN B:124 , LEU B:237 , TYR B:238 , PRO B:239 , GLN B:240 , THR B:241 , HOH B:299 , HOH B:318	BINDING SITE FOR RESIDUE GOL B 1
2	AC2	SOFTWARE	ARG A:115 , LYS A:167 , HOH A:329 , ARG C:2 , THR C:6 , HOH C:81 , HOH C:153	BINDING SITE FOR RESIDUE SO4 C 12
3	AC3	SOFTWARE	HOH B:19 , SER B:206 , ARG B:208 , ARG B:209	BINDING SITE FOR RESIDUE SO4 B 2

(no "SS Bond" information available for 3ME9)

(no "Cis Peptide Bond" information available for 3ME9)

(no "SAP(SNP)/Variant" information available for 3ME9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SGF29_C	PS51518	SGF29 C-terminal domain profile.	SGF29_HUMAN	152-293	2	A:152-287 B:152-291

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SGF29_C	PS51518	SGF29 C-terminal domain profile.	SGF29_HUMAN	152-293	2	A:152-287 B:152-291

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SGF29_C	PS51518	SGF29 C-terminal domain profile.	SGF29_HUMAN	152-293	1	A:152-287 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SGF29_C	PS51518	SGF29 C-terminal domain profile.	SGF29_HUMAN	152-293	1	- B:152-291

(no "Exon" information available for 3ME9)

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:174
 aligned with SGF29_HUMAN | Q96ES7 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:174
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283    
          SGF29_HUMAN   114 MRRGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVAC 287
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............................eeeeeee.....eeeeeeeeeeee....eeeeee........eeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------SGF29_C  PDB: A:152-287 UniProt: 152-293                                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3me9 A 114 GRRGVLmTLLQQSAmTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVAC 287
                                  |123    |  133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283    
                                  |     128-MSE                                                                                                                                                           
                                120-MSE

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with SGF29_HUMAN | Q96ES7 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:176
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
          SGF29_HUMAN   116 RGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACKEPK 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------DUF1325-3me9B01 B:157-289                                                                                                            -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------DUF1325-3me9B02 B:157-289                                                                                                            -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh..............................eeeeeee.....eeeeeeeeeeee....eeeeee.......eeeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------SGF29_C  PDB: B:152-291 UniProt: 152-293                                                                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3me9 B 116 RGVLmTLLQQSAmTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACKEPK 291
                                |  125  |    135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
                              120-MSE 128-MSE

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:8
         Q92133_XENLA     2 ARTKQTAR   9
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3me9 C   1 ARTkQTAR   8
                               |    
                               |    
                               4-M3L

Chain D from PDB  Type:PROTEIN  Length:4
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:4
         Q92133_XENLA     2 ARTK   5
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3me9 D   1 ARTk   4
                               |
                               4-M3L

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 3ME9)

(no "CATH Domain" information available for 3ME9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tudor (88)

Family: DUF1325 (10)

Homo sapiens (Human) (7)

1a	DUF1325-3me9B01	B:157-289
1b	DUF1325-3me9B02	B:157-289

Asymmetric Unit(hide GO term definitions)

Chain A,B (SGF29_HUMAN | Q96ES7)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0047485	protein N-terminus binding	Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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).
biological process
	GO:0071169	establishment of protein localization to chromatin	The directed movement of a protein to a part of a chromosome that is organized into chromatin.
	GO:0043966	histone H3 acetylation	The modification of histone H3 by the addition of an acetyl group.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005671	Ada2/Gcn5/Ada3 transcription activator complex	A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
	GO:0070461	SAGA-type complex	A histone acetyltransferase complex that acetylates nucleosomal H3 and H2B and is required for the expression of a subset of Pol II-transcribed genes. The budding yeast complex includes the acetyltransferase Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins.
	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.

Chain C,D (Q92133_XENLA | Q92133)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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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	SGF29_HUMAN \| Q96ES7
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UniProtKB/Swiss-Prot
	Q92133_XENLA \| Q92133	:	2hue 3gv6
	SGF29_HUMAN \| Q96ES7	:	3lx7 3mea 3met 3meu 3mev 3mew 5c0m
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	Q92133_XENLA \| Q92133	:	2l11 2l12 2l1b 3gl6 3h91 3mea 3met 3meu 3mev 3o7a 4hsu 4qeo

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