6XDJ: Crystal Structure Analysis of MBP-SIN3

Crystal Structure Analysis of MBP-SIN3. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Jun 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Serratia sp. (strain FS14), Saccharomyces cerevisiae
Chains: 4
Atoms: 13,335
Mol. weight: 197.46 kDa
Released: 16 Jun 2021

Explore 6XDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XDJ contains 108 α-helices and 100 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	7-11	5	1
α-helix	18-32	15
β-strand	35-39	5	1
α-helix	44-53	10
β-strand	60-64	5	1
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	2
α-helix	78-80	3
α-helix	84-87	4
β-strand	90	1	3
α-helix	92-97	6
β-strand	99-100	2	4
β-strand	103-104	2	4
β-strand	107-112	6	1
β-strand	115-119	5	5
β-strand	129	1	6
α-helix	133-141	9
β-strand	146-148	3	5
α-helix	155-164	10
β-strand	168-172	5	7
β-strand	177-183	7	7
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	5
α-helix	230-232	3
α-helix	233-237	5
β-strand	243-246	4	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	8
β-strand	254	1	8
α-helix	258	1
β-strand	259-260	2	9
β-strand	261-267	7	1
β-strand	268	1	2
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	1
β-strand	305	1	3
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	9
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-369	12
α-helix	371-372	2
α-helix	374-391	18
α-helix	398-412	15
α-helix	416-426	11
α-helix	432-438	7

Chain B: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	8-11	4	10
α-helix	18-32	15
β-strand	36-39	4	10
α-helix	44-52	9
β-strand	60-64	5	10
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	11
α-helix	78-80	3
α-helix	84-87	4
β-strand	90	1	12
α-helix	92-97	6
β-strand	99-100	2	13
β-strand	103-104	2	13
β-strand	107-112	6	10
β-strand	115-119	5	14
β-strand	129	1	15
α-helix	130-132	3
α-helix	133-141	9
β-strand	146-148	3	14
α-helix	155-164	10
β-strand	168-173	6	16
β-strand	176-183	8	16
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	14
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	14
α-helix	247-249	3
β-strand	250	1	15
β-strand	251	1	17
β-strand	254	1	17
α-helix	258	1
β-strand	259-260	2	18
β-strand	261-267	7	10
β-strand	268	1	11
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	10
β-strand	305	1	12
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	18
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-368	11
α-helix	372-373	2
α-helix	374-391	18
α-helix	398-409	12
α-helix	422-426	5
α-helix	431-440	10

Chain C: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	19
α-helix	18-32	15
β-strand	35-39	5	19
α-helix	44-52	9
β-strand	60-64	5	19
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	20
α-helix	78-80	3
α-helix	84-87	4
β-strand	90	1	21
α-helix	92-97	6
β-strand	99-100	2	22
β-strand	103-104	2	22
β-strand	107-112	6	19
β-strand	115-119	5	23
β-strand	129	1	24
α-helix	133-141	9
β-strand	146-148	3	23
α-helix	155-164	10
β-strand	168-172	5	25
β-strand	177-183	7	25
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	23
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	23
α-helix	247-249	3
β-strand	250	1	24
β-strand	251	1	26
β-strand	254	1	26
α-helix	258	1
β-strand	259-260	2	27
β-strand	261-267	7	19
β-strand	268	1	20
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-295	8
β-strand	302-303	2	19
β-strand	305	1	21
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	27
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-368	11
α-helix	372-373	2
α-helix	374-388	15

Chain D: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	28
α-helix	18-32	15
β-strand	36-39	4	28
α-helix	44-53	10
β-strand	60	1	28
β-strand	63-64	2	29
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	30
α-helix	78-80	3
α-helix	84-88	5
β-strand	90	1	31
α-helix	92-97	6
β-strand	99-100	2	32
β-strand	103-104	2	32
β-strand	107-112	6	29
β-strand	115-119	5	33
β-strand	129	1	34
α-helix	133-141	9
β-strand	146-148	3	33
α-helix	155-162	8
β-strand	168	1	35
β-strand	171-172	2	36
β-strand	177-178	2	36
β-strand	183	1	35
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	33
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	33
α-helix	247-249	3
β-strand	250	1	34
β-strand	251	1	37
β-strand	254	1	37
α-helix	258	1
β-strand	259-260	2	38
β-strand	261-265	5	29
α-helix	266	1
β-strand	267	1	28
β-strand	268	1	30
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	29
β-strand	305	1	31
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	38
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-369	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltodextrin-binding protein,Transcriptional regulatory protein SIN3	A, B, C, D	protein	443	Serratia sp. (strain FS14), Saccharomyces cerevisiae	P22579 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6XDJ_1 Maltodextrin-binding protein,Transcriptional regulatory protein SIN3 (chains A, B, C, D)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAAAKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVY
AQVTHLFQNAPDLLEDFKKFLPD

Primary citation

Crystal Structure Analysis of MBP-SIN3. Seo, H.-S. To be published.

Other PDB entries of the same protein (UniProt P22579 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6XAW 1.84 Å, Crystal Structure Analysis of SIN3-UME6
8HPO 2.6 Å, Cryo-EM structure of a SIN3/HDAC complex from budding yeast
8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
8KD3 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
8KD5 2.9 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
8KD4 2.93 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
8HXX 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S
9V2V 3.0 Å, Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
8KD2 3.02 Å, Rpd3S in complex with 187bp nucleosome
8KD6 3.07 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
8KD7 3.09 Å, Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
8HXY 3.1 Å, Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Browse structure collections

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