6WKR: PRC2-AEBP2-JARID2

PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome. Determined by electron microscopy at 3.5 Å resolution. Released 3 Feb 2021.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 18
Atoms: 29,296
Mol. weight: 623.91 kDa
Ligands: ZN, SAH, MG
Released: 3 Feb 2021

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

Secondary structure: helices and β-sheets

6WKR contains 108 α-helices and 155 β-strands across 17 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: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	84-106	23
α-helix	112-114	3
α-helix	135-146	12
β-strand	157-160	4	3
α-helix	162-163	2
β-strand	164-165	2	4
β-strand	184-192	9	5
β-strand	203-211	9	5
β-strand	230-233	4	3
α-helix	239-243	5
β-strand	245-253	9	5
β-strand	296-300	5	5
β-strand	315-318	4	4
β-strand	320	1	5
β-strand	354-357	4	4
β-strand	427-433	7	6
β-strand	439-444	6	6
β-strand	449	1	7
β-strand	456	1	7
α-helix	460-469	10
β-strand	474-475	2	8
β-strand	478	1	6
β-strand	484-489	6	6
β-strand	490-491	2	8
α-helix	505-507	3
α-helix	509	1
β-strand	525-528	4	9
α-helix	540-542	3
β-strand	557	1	9
β-strand	560	1	9
β-strand	566	1	10
β-strand	573	1	10
α-helix	590-601	12
α-helix	608-624	17
α-helix	629-631	3
α-helix	632-650	19
α-helix	653-665	13
α-helix	671-681	11

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	109-111	3
α-helix	113-114	2
α-helix	146-150	5
α-helix	162-165	4

Chain C: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	19-60	42
α-helix	66-68	3
β-strand	82-84	3	30
β-strand	86-87	2	11
β-strand	95-97	3	30
β-strand	99-100	2	13
β-strand	114-115	2	31
β-strand	120-121	2	32
α-helix	139-142	4
α-helix	144-152	9
α-helix	169-177	9
α-helix	222-230	9
α-helix	237-249	13
α-helix	274-284	11
β-strand	285-286	2	33
β-strand	291-292	2	33
α-helix	329-337	9
α-helix	434-447	14
α-helix	451-457	7
α-helix	463-472	10
α-helix	474-476	3
α-helix	478-480	3
α-helix	492-495	4
α-helix	497-510	14
α-helix	511-513	3
α-helix	535-538	4
α-helix	572-575	4
α-helix	605-608	4
β-strand	614-618	5	34
β-strand	624-628	5	34
β-strand	632	1	35
β-strand	637-640	4	36
β-strand	644-647	4	32
α-helix	648-661	14
β-strand	667-668	2	32
β-strand	673-676	4	32
β-strand	680-681	2	31
α-helix	683-686	4
α-helix	687	1
β-strand	688	1	37
α-helix	689	1
β-strand	695-702	8	36
β-strand	705-712	8	36
β-strand	716	1	35
β-strand	721	1	34
β-strand	723	1	37
α-helix	730-736	7

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	25-35	11
α-helix	47-50	4
α-helix	52-55	4

Chain F: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	50
β-strand	12-16	5	50
β-strand	22	1	51
α-helix	23-34	12
β-strand	41-45	5	52
β-strand	48-49	2	52
β-strand	55	1	51
β-strand	65-67	3	50
β-strand	68-71	4	52

Chain I: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	32
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	42
α-helix	86-113	28
β-strand	118-119	2	43
α-helix	121-131	11

Chain J: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	43
α-helix	50-75	26
β-strand	80-81	2	42
α-helix	83-93	11
β-strand	98	1	44

Chain K: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	45
α-helix	46-72	27
α-helix	80-87	8
α-helix	91-96	6
β-strand	101-102	2	46

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	F, T	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Polycomb protein SUZ12	A	protein	739	Homo sapiens	Q15022 (AlphaFold model)
Polycomb protein EED	L	protein	441	Homo sapiens	O75530 (AlphaFold model)
Histone-binding protein RBBP4	N	protein	425	Homo sapiens	Q09028 (AlphaFold model)
Histone-lysine N-methyltransferase EZH2	C	protein	746	Homo sapiens	Q15910
Protein Jumonji	B, E	protein	450	Homo sapiens	Q92833
Zinc finger protein AEBP2	P	protein	295	Homo sapiens	Q6ZN18
DNA (314-mer)	H	DNA	320	Homo sapiens
Histone H3.2	I, O	protein	136	Xenopus laevis	P84233
Histone H4	J, Q	protein	103	Xenopus laevis	P62799
Histone H2A type 1	K, R	protein	130	Xenopus laevis	P06897
Histone H2B 1.1	M, S	protein	126	Xenopus laevis	P02281

Sequence of entity 1 (F, T), FASTA

>6WKR_1 Ubiquitin (chains F, T)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 2 (A), FASTA

>6WKR_2 Polycomb protein SUZ12 (chains A)
MAPQKHGGGGGGGSGPSAGSGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSA
AAAAGAAVLPVKKPKMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSH
RNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQN
SVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPS
NSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMT
VFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLR
WTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPN
ENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVY
HPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASM
SEFLESEDGEVEQQRTYSSGHNRLYFHSDTCLPLRPQEMEVDSEDEKDPEWLREKTITQI
EEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNLCRNFMLHL
VSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEK
ALETDSVSGVSKQSKKQKL

Sequence of entity 3 (L), FASTA

>6WKR_3 Polycomb protein EED (chains L)
MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTP
NAPGRKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNR
VTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITM
QCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL
SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFS
TRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQ
CDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSR
DSSILIAVCDDASIWRWDRLR

Sequence of entity 4 (N), FASTA

>6WKR_4 Histone-binding protein RBBP4 (chains N)
MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKD
FSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIK
INHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEG
YGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE
SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
WDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAE
DGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
EGQGS

Sequence of entity 5 (C), FASTA

>6WKR_5 Histone-lysine N-methyltransferase EZH2 (chains C)
MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEW
KQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNF
MVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQ
YNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEEL
KEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH
ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPN
NSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSEANSRCQTPIKM
KPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPA
PAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQ
NFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS
CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK
YMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGE
ELFFDYRYSQADALKYVGIEREMEIP

Sequence of entity 6 (B, E), FASTA

>6WKR_6 Protein Jumonji (chains B, E)
MSKERPKRNIIQKKYDDSDGIPWSEERVVRKVLYLSLKEFKNSQKRQHAEGIAGSLKTVN
GLLGNDQSKGLGPASEQSENEKDDASQVSSTSNDVSSSDFEEGPSRKRPRLQAQRKFAQS
QPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQ
DEEEVEEEDDETEDVKTATNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQK
HKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGSSAKGLAATHHHPPLHRSAQDLR
KQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVKDT
KPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTK
EVGGRQLREGLQLREGLRNSKRRLEEAHQA

Sequence of entity 7 (P), FASTA

>6WKR_7 Zinc finger protein AEBP2 (chains P)
MSSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQC
QACFNSSPDLADHIRSIHVDGQRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPF
KCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEESPSKAGMNKRRKLKNKRR
RSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLL
LHWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR

Sequence of entity 8 (H), FASTA

>6WKR_8 DNA (314-MER) (chains H)
CAGGATGTATATATCTGAGACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTTAA
ACGCGGGGGACAGCGCGTACGTGCGTTTTAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTGGGCACCGGGATTCTCCAGCCGCCGGCAGCNNNNNNGCTGCCGGCGGCTGGAG
AATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCAC
GTACGCGCTGTCCCCCGCGTTTAAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACG
TCTCAGATATATACATCCTG

Sequence of entity 9 (I, O), FASTA

>6WKR_9 Histone H3.2 (chains I, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 10 (J, Q), FASTA

>6WKR_10 Histone H4 (chains J, Q)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 11 (K, R), FASTA

>6WKR_11 Histone H2A type 1 (chains K, R)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKC
TESAKSAKSK

Sequence of entity 12 (M, S), FASTA

>6WKR_12 Histone H2B 1.1 (chains M, S)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
MG	Magnesium ion	Mg	1

Primary citation

JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Kasinath, V., Beck, C., Sauer, P. et al. Science (2021) 371. DOI 10.1126/science.abc3393 · PubMed

Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant

Browse structure collections

About this viewer

MolViewer shows 6WKR 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.