6CW3: Antibody heavy chain

Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2. Determined by X-ray diffraction at 1.98 Å resolution. Released 19 Sept 2018.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae S288c
Chains: 8
Atoms: 11,837
Mol. weight: 183.55 kDa
Ligands: ZN
Released: 19 Sept 2018

Explore 6CW3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CW3 contains 68 α-helices and 118 β-strands across 8 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: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	21-28	8	1
α-helix	32-34	3
β-strand	37-42	6	3
β-strand	48-55	8	3
β-strand	60-63	4	3
β-strand	71-76	6	1
α-helix	77-79	3
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-102	8	3
β-strand	108	1	4
β-strand	113-116	4	3
β-strand	120-122	3	3
β-strand	123-124	2	2
α-helix	127-129	3
β-strand	130	1	5
α-helix	131-132	2
β-strand	133-137	5	6
β-strand	148-158	11	6
β-strand	159	1	5
β-strand	164-167	4	7
β-strand	169	1	8
β-strand	171	1	8
β-strand	176-178	3	6
α-helix	179-181	3
β-strand	182-183	2	6
β-strand	189-198	10	6
α-helix	199-201	3
β-strand	208-213	6	7
α-helix	214-216	3
β-strand	218-223	6	7

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	9
α-helix	7-9	3
β-strand	10-14	5	10
β-strand	20-24	5	11
β-strand	34-39	6	10
β-strand	46-50	5	10
β-strand	54-55	2	10
α-helix	56	1
β-strand	63-68	6	11
β-strand	71-76	6	11
α-helix	81-83	3
β-strand	86-91	6	10
α-helix	94-96	3
β-strand	98-99	2	10
β-strand	103-107	5	10
β-strand	112	1	12
α-helix	113-114	2
β-strand	115-119	5	13
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	13
β-strand	141	1	12
β-strand	146-151	6	14
β-strand	154-157	4	14
β-strand	160-164	5	13
α-helix	165-168	4
β-strand	174-183	10	13
α-helix	184-187	4
β-strand	192-198	7	14
β-strand	206-211	6	14

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	14-15	2	16
β-strand	21-28	8	15
α-helix	32-34	3
β-strand	36-42	7	17
β-strand	48-55	8	17
β-strand	60-63	4	17
β-strand	71-76	6	15
α-helix	77-79	3
β-strand	81-86	6	15
α-helix	91-93	3
β-strand	95-102	8	17
β-strand	108	1	18
β-strand	113-116	4	17
β-strand	120-122	3	17
β-strand	123-124	2	16
α-helix	127-129	3
β-strand	130	1	19
α-helix	131-132	2
β-strand	133-137	5	20
β-strand	148-158	11	20
β-strand	159	1	19
β-strand	164-167	4	21
α-helix	168-170	3
β-strand	176-178	3	20
α-helix	179-181	3
β-strand	182-183	2	20
β-strand	189-198	10	20
α-helix	199-201	3
β-strand	208-213	6	21
α-helix	214-216	3
β-strand	218-223	6	21
α-helix	226-228	3

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	9
α-helix	7-9	3
β-strand	10-14	5	22
β-strand	20-24	5	14
β-strand	34-39	6	22
β-strand	46-50	5	22
β-strand	54-55	2	22
α-helix	56	1
β-strand	63-68	6	14
β-strand	71-76	6	14
α-helix	81-83	3
β-strand	86-91	6	22
α-helix	94-96	3
β-strand	98	1	22
β-strand	103-107	5	22
β-strand	112	1	23
α-helix	113-114	2
β-strand	115-119	5	24
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	24
β-strand	141	1	23
β-strand	146-151	6	11
β-strand	154-157	4	11
β-strand	160-164	5	24
α-helix	165-168	4
β-strand	174-183	10	24
α-helix	184-188	5
β-strand	192-198	7	11
β-strand	206-211	6	11

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	27
β-strand	13	1	27
β-strand	19-22	4	26
β-strand	29-30	2	26
α-helix	32-36	5
β-strand	50-53	4	26
α-helix	67-80	14
α-helix	85-92	8
α-helix	97-104	8
α-helix	105-109	5

Chain F: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	101-105	5	25
α-helix	111-127	17
α-helix	133-141	9
β-strand	146-151	6	25
β-strand	157-166	10	25
α-helix	167-169	3
β-strand	171-179	9	25
α-helix	192-203	12
β-strand	208-212	5	25
α-helix	219-222	4
β-strand	226-227	2	25
α-helix	234-237	4
β-strand	249-253	5	25
β-strand	258	1	18
α-helix	260-262	3
α-helix	263-279	17
α-helix	286-287	2
β-strand	288	1	26
α-helix	289-291	3
α-helix	292-294	3
α-helix	297-299	3
α-helix	302-304	3
α-helix	310-313	4

Chain G: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	30
β-strand	13	1	30
β-strand	19-22	4	29
β-strand	29-31	3	29
α-helix	32-36	5
β-strand	50-53	4	29
α-helix	101-104	4
α-helix	105-109	5

Chain H: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	100-104	5	28
α-helix	111-127	17
α-helix	135-140	6
β-strand	146-152	7	28
β-strand	156-166	11	28
α-helix	167-169	3
β-strand	171-176	6	28
α-helix	189-203	15
β-strand	208-211	4	28
α-helix	222-224	3
β-strand	226-227	2	28
α-helix	234-236	3
β-strand	250-253	4	28
β-strand	258	1	4
α-helix	260-262	3
α-helix	263-279	17
β-strand	288	1	29
α-helix	289-291	3
α-helix	292-294	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody heavy chain	A, C	protein	234	Homo sapiens
antibody light chain	B, D	protein	215	Homo sapiens
Histone acetyltransferase GCN5	F, H	protein	254	Saccharomyces cerevisiae S288c	Q03330 (AlphaFold model)
Transcriptional adapter 2	E, G	protein	122	Saccharomyces cerevisiae S288c	Q02336 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6CW3_1 antibody heavy chain (chains A, C)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSYIHWVRQAPGKGLEWVASIYSYYGS
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWQGMYEMGYGMDYWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B, D), FASTA

>6CW3_2 antibody light chain (chains B, D)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQGWANLITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (F, H), FASTA

>6CW3_3 Histone acetyltransferase GCN5 (chains F, H)
MGSVTDVEKGIVKFEFDGVEYTFKERPSVVEENEGKIEFRVVNNDNTKENMMVLTGLKNI
FQKQLPKMPKEYIARLVYDRSHLSMAVIRKPLTVVGGITYRPFDKREFAEIVFCAISSTE
QVRGYGAHLMNHLKDYVRNTSNIKYFLTYADNYAIGYFKKQGFTKEITLDKSIWMGYIKD
YEGGTLMQCSMLPRIRYLDAGKILLLQEAALRRKIRTISKSHIVRPGLEQFKDLNNIKPI
DPMTIPGLKEAGWT

Sequence of entity 4 (E, G), FASTA

>6CW3_4 Transcriptional adapter 2 (chains E, G)
GSNKFHCDVCSADCTNRVRVSCAICPEYDLCVPCFSQGSYTGKHRPYHDYRIIETNSYPI
LCPDWGADEELQLIKGAQTLGLGNWQDIADHIGSRGKEEVKEHYLKYYLESKYYPIPDIT
AG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Sun, J., Paduch, M., Kim, S.A. et al. Proc Natl Acad Sci U S A (2018) 115:10010-10015. DOI 10.1073/pnas.1805343115 · PubMed

Other PDB entries of the same protein (UniProt Q03330 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1E6I 1.87 Å, Bromodomain from GCN5 complexed with acetylated H4 peptide
1YGH 1.9 Å, Hat domain of GCN5 from saccharomyces cerevisiae
6CW2 2.67 Å, Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex,…

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