6BX3: Histone H3k4 methyltransferase

Structure of histone H3k4 methyltransferase. Determined by electron microscopy at 4.3 Å resolution. Released 5 Sept 2018.

Method: Electron microscopy
Resolution: 4.3 Å
Organisms: Saccharomyces cerevisiae (strain YJM789), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 7
Atoms: 10,456
Mol. weight: 199.98 kDa
Released: 5 Sept 2018

Explore 6BX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BX3 contains 36 α-helices and 92 β-strands across 7 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: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	24
β-strand	32	1	25
β-strand	35	1	25
β-strand	40	1	24
β-strand	47	1	24
α-helix	57-58	2
β-strand	61-62	2	26
β-strand	69-73	5	26
β-strand	79-83	5	26
β-strand	92	1	26
α-helix	98-99	2
β-strand	102-104	3	27
β-strand	110-113	4	27
β-strand	115	1	28
β-strand	120-124	5	27
β-strand	129-134	6	27
β-strand	141-143	3	28
β-strand	154	1	29
β-strand	157-158	2	28
β-strand	162-163	2	30
β-strand	166	1	29
β-strand	177-178	2	30
β-strand	195	1	31
β-strand	204-207	4	31
α-helix	208	1
β-strand	213-216	4	31
β-strand	223-227	5	31
β-strand	245	1	32
β-strand	248-250	3	33
β-strand	254-257	4	33
α-helix	258	1
α-helix	264-266	3
β-strand	267-268	2	33
β-strand	275	1	33
β-strand	292	1	32
β-strand	295	1	34
β-strand	300	1	34
β-strand	303	1	32
β-strand	304	1	35
β-strand	308	1	35
β-strand	314	1	34

Chain B: 4 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	12
β-strand	29-34	6	13
β-strand	41-45	5	13
β-strand	79-80	2	14
β-strand	86-88	3	14
β-strand	95-98	4	15
β-strand	99-100	2	14
β-strand	109-112	4	15
β-strand	120-122	3	16
β-strand	130-132	3	16
β-strand	141-143	3	16
β-strand	151-152	2	16
β-strand	173-176	4	17
β-strand	184-187	4	17
β-strand	193-196	4	17
β-strand	199	1	18
β-strand	203	1	18
β-strand	206-209	4	17
β-strand	222	1	19
β-strand	228	1	20
β-strand	229	1	19
β-strand	242	1	20
α-helix	243-244	2
β-strand	245	1	21
β-strand	248	1	21
β-strand	269-274	6	22
β-strand	281-286	6	22
β-strand	295	1	23
β-strand	297-298	2	22
β-strand	307	1	23
β-strand	315-320	6	12
β-strand	327-331	5	12
β-strand	337-339	3	12
α-helix	343-345	3
α-helix	356-358	3
α-helix	404-406	3

Chain E: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	800-823	24
α-helix	926-932	7
β-strand	967	1	1
α-helix	975-987	13
β-strand	995	1	2
β-strand	1003	1	2
β-strand	1016	1	3
β-strand	1023-1026	4	4
β-strand	1036	1	1
β-strand	1037-1041	5	4
α-helix	1048-1050	3
β-strand	1051	1	3
β-strand	1052	1	4

Chain F: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	118-128	11
α-helix	136-144	9
α-helix	151-157	7
α-helix	165-170	6
α-helix	184-185	2
α-helix	192-199	8
α-helix	203-207	5
α-helix	209-240	32
α-helix	279-282	4
α-helix	312-348	37

Chain K: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	99-101	3
α-helix	103-105	3
α-helix	121-124	4
β-strand	128	1	5
β-strand	136	1	6
β-strand	137-139	3	7
β-strand	186	1	8
β-strand	187	1	9
α-helix	197-199	3
β-strand	204-205	2	8
β-strand	212	1	10
β-strand	214-215	2	8
α-helix	221	1
β-strand	222	1	10
α-helix	223	1
β-strand	233	1	11
β-strand	234	1	6
β-strand	359	1	11
β-strand	436	1	5
β-strand	437	1	9
β-strand	448-450	3	7
α-helix	460-462	3
α-helix	480-499	20

Chain M: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	134-143	10
α-helix	153-161	9

Chain N: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	123-128	6
α-helix	131-141	11
α-helix	153-158	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase, H3 lysine-4 specific	E	protein	278	Saccharomyces cerevisiae (strain YJM789)	A6ZT27 (AlphaFold model)
COMPASS component BRE2	K	protein	417	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P43132 (AlphaFold model)
COMPASS component SDC1	M, N	protein	42	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q03323 (AlphaFold model)
COMPASS component SPP1	F	protein	237	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q03012 (AlphaFold model)
COMPASS component SWD1	B	protein	412	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P39706
COMPASS component SWD3	A	protein	314	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38123

Sequence of entity 1 (E), FASTA

>6BX3_1 Histone-lysine N-methyltransferase, H3 lysine-4 specific (chains E)
KIWQSRRKTLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRKVTDKLKINYLPHRRRV
HQPLNTVNIHNERNEYTPELCQREESSNKEPSDSVPQEVSSSRDNRASNRRFQQDIEAQK
AAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKEMIIEYVGERIRQPVAE
MREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPNCTAKIIKVGGRRRIVI
YALRDIAASEELTYDYKFEREKDDEERLPCLCGAPNCK

Sequence of entity 2 (K), FASTA

>6BX3_2 COMPASS component BRE2 (chains K)
FDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWRTARSDVCIKEGMTYWEVEVIRGGNKK
FADGVNNKENADDSVDEVQSGIYEKMHKQVNDTPHLRFGVCRREASLEAPVGFDVYGYGI
RDISLESIHEGKLNCVLENGSPLKEGDKIGFLLSLPSIHTQIKQAKEFTKRRIFALNSHM
DTMNEPWREDAENGPSRKKLKQETTNKEFQRALLEDIEYNDVVRDQIAIRYKNQLFFEAT
DYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQNGKYLGKAFENLKPLLPPFSELQYNEK
FYLGYWQHGEARDESNDKNTTSAKKKKQQQKKKKGLILRNKYVNNNKLGYYPTISCFNGG
TARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDTLYKEQIAEDIVWDIIDELEQIAL

Sequence of entity 3 (M, N), FASTA

>6BX3_3 COMPASS component SDC1 (chains M, N)
TRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNI

Sequence of entity 4 (F), FASTA

>6BX3_4 COMPASS component SPP1 (chains F)
HGREFVNDIWSRLKTDEDRAVVKKMVEQTGHIDKFKKFGQLDFIDNNIVVKTDDEKEIFD
QIVVRDMTLKTLEDDLQEVQEISLPLFKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVE
CGKEDSKGTKRKKKKNSSRSRARKNICGYCSTYERIPCSVEEFVRDFGSNEEATKIHEVC
TKWKCNRHLDWVSTNQEQYLQQIDSLESMQERLQHLIQARKKQLNIQYYEEILRRGL

Sequence of entity 5 (B), FASTA

>6BX3_5 COMPASS component SWD1 (chains B)
NILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRPI
CVPGNMLGAHVRPITSIAWSPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGCQ
WLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEKQLSSTPDHGYVLVCTVHTKHP
NIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQY
EISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETTS
GTLVRVLEGAEEELIDINWDFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEEN
VDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYDVRGNNLLVERFTI

Sequence of entity 6 (A), FASTA

>6BX3_6 COMPASS component SWD3 (chains A)
FQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSEL
CWSPDGQCIATASDDFSVEIIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESIK
IWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYDGLIRIFDAETGHCLKTLTYDK
DWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHSC
GMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIMC
SLALNGDCCLWRWV

Primary citation

Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex. Qu, Q., Takahashi, Y.H., Yang, Y. et al. Cell (2018) 174:1117-1126.e12. DOI 10.1016/j.cell.2018.07.020 · PubMed

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