7AOA: Methyl-CpG-binding domain protein 2

Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex. Determined by electron microscopy at 19.4 Å resolution. Released 11 Nov 2020.

Method: Electron microscopy
Resolution: 19.4 Å
Organism: Homo sapiens
Chains: 7
Atoms: 18,153
Mol. weight: 412.52 kDa
Ligands: IHP, ZN
Released: 11 Nov 2020

Explore 7AOA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AOA contains 84 α-helices and 124 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.

Chains A and D: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	6
α-helix	22	1
β-strand	23-32	10	6
β-strand	38-46	9	6
α-helix	47	1
β-strand	107	1	7
β-strand	109-118	10	6
α-helix	119-121	3
β-strand	122-126	5	6
β-strand	127-130	4	7
α-helix	131-136	6
β-strand	146-149	4	7
β-strand	152-153	2	6
α-helix	175-182	8
α-helix	191-193	3
β-strand	195-199	5	8
α-helix	207-226	20
α-helix	238-245	8
α-helix	248-260	13
α-helix	265-272	8
α-helix	284-287	4
α-helix	290-303	14
α-helix	307-313	7
α-helix	320-330	11
β-strand	472-473	2	9
α-helix	477-485	9
α-helix	487-490	4
α-helix	492-495	4
α-helix	502-503	2
α-helix	505-514	10
α-helix	534-543	10

Chains B and E: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	8
α-helix	17-20	4
α-helix	33-44	12
α-helix	48-50	3
β-strand	52-56	5	8
α-helix	57-60	4
α-helix	61-64	4
α-helix	70-78	9
α-helix	84-93	10
α-helix	106-125	20
β-strand	131-134	4	8
β-strand	143	1	14
β-strand	146	1	14
β-strand	148	1	15
β-strand	151	1	15
α-helix	155-163	9
β-strand	170-174	5	8
α-helix	181-186	6
β-strand	193-200	8	8
α-helix	217-219	3
β-strand	223-228	6	8
α-helix	234-252	19
β-strand	256-260	5	8
β-strand	266	1	16
β-strand	276	1	16
α-helix	278-290	13
β-strand	295-298	4	8
α-helix	305-319	15
β-strand	327	1	17
α-helix	328-330	3
α-helix	334-336	3
β-strand	342	1	17
α-helix	356-371	16

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	150-151	2	1
β-strand	160-165	6	1
β-strand	175-180	6	1
β-strand	186-187	2	1
α-helix	190-197	8
α-helix	198-200	3

Chain F: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	5
β-strand	44	1	18
β-strand	49-54	6	19
β-strand	61-66	6	19
β-strand	68-69	2	19
β-strand	70	1	18
β-strand	77-87	11	19
β-strand	108	1	5
β-strand	116-123	8	19
β-strand	129-133	5	20
β-strand	136-143	8	20
β-strand	149-153	5	20
α-helix	161-162	2
β-strand	171-173	3	20
β-strand	183-185	3	21
β-strand	192-195	4	21
β-strand	202-206	5	21
β-strand	216-217	2	20
β-strand	221-223	3	21
β-strand	230-235	6	22
β-strand	242-247	6	22
β-strand	251-256	6	22
β-strand	267-270	4	22
β-strand	276-281	6	23
β-strand	288-293	6	23
β-strand	297-302	6	23
β-strand	311-314	4	23
β-strand	320-325	6	24
β-strand	332-337	6	24
β-strand	342-346	5	24
α-helix	347-349	3
α-helix	356-359	4
β-strand	366-370	5	24
β-strand	377-382	6	5
β-strand	389-394	6	5
β-strand	398-404	7	5

Chain G: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21
β-strand	32-39	8	9
β-strand	44	1	25
β-strand	49-54	6	26
β-strand	61-66	6	26
β-strand	68-69	2	26
β-strand	70	1	25
β-strand	77-87	11	26
β-strand	108	1	9
β-strand	116-123	8	26
β-strand	129-132	4	27
β-strand	139-143	5	27
β-strand	149-153	5	27
α-helix	161-162	2
β-strand	171-173	3	27
β-strand	183-185	3	28
β-strand	192-195	4	28
β-strand	202-206	5	28
β-strand	216-217	2	27
β-strand	221-223	3	28
β-strand	230-235	6	29
β-strand	242-247	6	29
β-strand	251-256	6	29
β-strand	267-270	4	29
β-strand	276-281	6	30
β-strand	288-293	6	30
β-strand	297-302	6	30
β-strand	311-314	4	30
β-strand	320-325	6	31
β-strand	332-337	6	31
β-strand	342-346	5	31
α-helix	347-349	3
α-helix	356-359	4
β-strand	366-370	5	31
β-strand	377-382	6	9
β-strand	389-394	6	9
β-strand	398-404	7	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyl-CpG-binding domain protein 2	C	protein	411	Homo sapiens	Q9UBB5 (AlphaFold model)
Metastasis-associated protein MTA1	A, D	protein	715	Homo sapiens	Q13330 (AlphaFold model)
Histone deacetylase 1	B, E	protein	482	Homo sapiens	Q13547 (AlphaFold model)
Histone-binding protein RBBP4	F, G	protein	425	Homo sapiens	Q09028 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7AOA_1 Methyl-CpG-binding domain protein 2 (chains C)
MRAHPGGGRCCPEQEEGESAAGGSGAGGDSAIEQGGQGSALAPSPVSGVRREGARGGGRG
RGRWKQAGRGGGVCGRGRGRGRGRGRGRGRGRGRGRPPSGGSGLGGDGGGCGGGGSGGGG
APRREPVPFPSGSAGPGPRGPRATESGKRMDCPALPPGWKKEEVIRKSGLSAGKSDVYYF
SPSGKKFRSKPQLARYLGNTVDLSSFDFRTGKMMPSKLQKNKQRLRNDPLNQNKGKPDLN
TTLPIRQTASIFKQPVTKVTNHPSNKVKSDPQRMNEQPRQLFWEKRLQGLSASDVTEQII
KTMELPKGLQGVGPGSNDETLLSAVASALHTSSAPITGQVSAAVEKNPAVWLNTSQPLCK
AFIVTDEDIRKQEERVQQVRKKLEEALMADILSRAADTEEMDIEMDSGDEA

Sequence of entity 2 (A, D), FASTA

>7AOA_2 Metastasis-associated protein MTA1 (chains A, D)
MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTANGNVEAKVVCFYRRRDISSTLIALAD
KHATLSVCYKAGPGADNGEEGEIEEEMENPEMVDLPEKLKHQLRHRELFLSRQLESLPAT
HIRGKCSVTLLNETESLKSYLEREDFFFYSLVYDPQQKTLLADKGEIRVGNRYQADITDL
LKEGEEDGRDQSRLETQVWEAHNPLTDKQIDQFLVVARSVGTFARALDCSSSVRQPSLHM
SAAAASRDITLFHAMDTLHKNIYDISKAISALVPQGGPVLCRDEMEEWSASEANLFEEAL
EKYGKDFTDIQQDFLPWKSLTSIIEYYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPNYN
KPNPNQISVNNVKAGVVNGTGAPGQSPGAGRACESCYTTQSYQWYSWGPPNMQCRLCASC
WTYWKKYGGLKMPTRLDGERPGPNRSNMSPHGLPARSSGSPKFAMKTRQAFYLHTTKLTR
IARRLCREILRPWHAARHPYLPINSAAIKAECTARLPEASQSPLVLKQAVRKPLEAVLRY
LETHPRPPKPDPVKSVSSVLSSLTPAKVAPVINNGSPTILGKRSYEQHNGVDGNMKKRLL
MPSRGLANHGQARHMGPSRNLLLNGKSYPTKVRLIRGGSLPPVKRRRMNWIDAPDDVFYM
ATEETRKIRKLLSSSETKRAARRPYKPIALRQSQALPPRPPPPAPVNDEPIVIED

Sequence of entity 3 (B, E), FASTA

>7AOA_3 Histone deacetylase 1 (chains B, E)
MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN
AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS
AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG
DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI
FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG
GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE
KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF
SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK
LA

Sequence of entity 4 (F, G), FASTA

>7AOA_4 Histone-binding protein RBBP4 (chains F, G)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (K) are not listed.

Primary citation

The topology of chromatin-binding domains in the NuRD deacetylase complex. Millard, C.J., Fairall, L., Ragan, T.J. et al. Nucleic Acids Res (2020) 48:12972-12982. DOI 10.1093/nar/gkaa1121 · PubMed

Other PDB entries of the same protein (UniProt Q9UBB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MWM 1.6 Å, Crystal structure of MBD2 with DNA
7RAY 1.78 Å, Crystal structure of MBD2 with DNA
6C1T 1.84 Å, MBD2 in complex with a partially methylated DNA
6C1A 2.05 Å, MBD2 in complex with methylated DNA
6CNP 2.1 Å, Crystal structure of MBD2 complex with methylated CpG island
6CNQ 2.15 Å, MBD2 in complex with methylated DNA
6C1U 2.3 Å, MBD2 in complex with a deoxy-oligonucleotide
6C1V 2.3 Å, MBD2 in complex with double-stranded DNA
7MWK 2.45 Å, Crystal structure of MBD2 with DNA
6C2F 2.65 Å, MBD2 in complex with methylated DNA
7AO8 4.5 Å, Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex
7AO9 6.1 Å, Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

Browse structure collections

About this viewer

MolViewer shows 7AOA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.