9RWZ: ZSWIM8-CUL3 complex

Name: PDB 9RWZ: ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Published: 2026-03-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO. Determined by electron microscopy at 3.1 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 11
Atoms: 28,601
Mol. weight: 689.96 kDa
Ligands: ZN
Released: 18 Mar 2026

Explore 9RWZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RWZ contains 185 α-helices and 94 β-strands across 9 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: 26 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	1
β-strand	44-48	5	2
β-strand	53-62	10	3
α-helix	68-81	14
β-strand	93-94	2	3
β-strand	100-102	3	3
β-strand	113-119	7	3
β-strand	126-139	14	3
α-helix	140-146	7
α-helix	157-166	10
α-helix	168-173	6
β-strand	175-177	3	2
β-strand	180-183	4	2
β-strand	191	1	2
β-strand	196-208	13	2
β-strand	213-225	13	2
β-strand	229	1	4
α-helix	230-237	8
α-helix	253-257	5
α-helix	258-262	5
β-strand	266-268	3	4
β-strand	279-280	2	4
β-strand	281-288	8	5
β-strand	293-297	5	6
β-strand	303-307	5	6
α-helix	308-314	7
β-strand	326-331	6	5
β-strand	335-339	5	5
β-strand	345-346	2	4
α-helix	347	1
β-strand	351	1	2
α-helix	358-368	11
α-helix	372-385	14
α-helix	392-397	6
β-strand	400-401	2	2
β-strand	406-412	7	1
β-strand	418-419	2	7
β-strand	427-428	2	7
β-strand	431	1	8
β-strand	434	1	8
β-strand	444	1	9
β-strand	448	1	10
β-strand	450	1	11
β-strand	453-455	3	12
α-helix	464-479	16
β-strand	480	1	13
β-strand	482	1	13
β-strand	485	1	10
β-strand	492-494	3	12
α-helix	501-511	11
β-strand	515	1	11
β-strand	519-522	4	12
α-helix	528-534	7
α-helix	535-540	6
β-strand	545-548	4	12
α-helix	550-553	4
α-helix	557-571	15
β-strand	574	1	9
β-strand	577-578	2	7
β-strand	591-599	9	1
β-strand	611-617	7	1
β-strand	625-631	7	1
α-helix	642-657	16
β-strand	663-669	7	1
α-helix	673-675	3
α-helix	676-692	17
β-strand	701-708	8	1
β-strand	715-717	3	1
β-strand	724	1	14
β-strand	729	1	14
α-helix	730-731	2
β-strand	734-736	3	1
β-strand	747-751	5	1
β-strand	763-770	8	1
α-helix	776-786	11
β-strand	795	1	8
α-helix	801-816	16
α-helix	847-849	3
α-helix	850-852	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
β-strand	12-18	7	15
α-helix	24-34	11
α-helix	39-41	3
β-strand	45-46	2	16
β-strand	49-50	2	16
α-helix	72	1
β-strand	73-75	3	15
β-strand	76	1	16
β-strand	80	1	17
β-strand	85	1	17
α-helix	92-96	5

Chain C: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	18
β-strand	10	1	19
β-strand	12-19	8	18
α-helix	24-34	11
α-helix	39-41	3
β-strand	45-46	2	20
β-strand	49-50	2	20
α-helix	51-52	2
β-strand	73-75	3	18
β-strand	80	1	21
β-strand	85	1	21
β-strand	90	1	19
α-helix	94-96	3

Chain D: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	18
β-strand	28-32	5	18
α-helix	41-47	7
α-helix	53-57	5
β-strand	59-61	3	18
α-helix	67-82	16
α-helix	90-93	4
α-helix	100-110	11

Chain E: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	15
β-strand	28-32	5	15
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	15
α-helix	67-82	16
α-helix	91-94	4
α-helix	97-99	3
α-helix	100-110	11

Chain H: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	17	1
β-strand	18-20	3	22
α-helix	21-26	6
α-helix	27-44	18
α-helix	54-66	13
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-95	6
α-helix	102-122	21
α-helix	124-134	11
α-helix	139-147	9
α-helix	148-152	5
α-helix	155-174	20
α-helix	181-186	6

Chain I: 13 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	18-20	3	23
α-helix	21-22	2
α-helix	24-26	3
α-helix	27-45	19
α-helix	54-66	13
α-helix	71-84	14
α-helix	85-90	6
α-helix	91-95	5
α-helix	101-122	22
α-helix	124-134	11
α-helix	139-147	9
α-helix	148-152	5
α-helix	158-173	16
α-helix	181-187	7

Chain M: 57 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	73-75	3
α-helix	76-86	11
α-helix	90-93	4
α-helix	99-100	2
α-helix	102-110	9
α-helix	118-126	9
α-helix	132-142	11
β-strand	146-152	7	26
β-strand	155-160	6	26
β-strand	173-178	6	26
β-strand	183-187	5	26
α-helix	198-209	12
β-strand	215-217	3	26
α-helix	220-224	5
α-helix	229-242	14
α-helix	248-258	11
α-helix	265-268	4
β-strand	271-273	3	22
α-helix	291-295	5
α-helix	296-306	11
α-helix	327-336	10
α-helix	345-359	15
α-helix	365-378	14
α-helix	380-389	10
α-helix	410-431	22
α-helix	438-462	25
α-helix	476-481	6
α-helix	769-782	14
α-helix	786-802	17
α-helix	824-844	21
α-helix	853-862	10
α-helix	867-869	3
α-helix	872-888	17
α-helix	889-891	3
α-helix	896-910	15
α-helix	923-933	11
α-helix	951-964	14
α-helix	976-996	21
α-helix	1004-1011	8
α-helix	1235-1251	17
β-strand	1260	1	12
α-helix	1273-1274	2
α-helix	1278-1295	18
α-helix	1299-1301	3
α-helix	1306-1314	9
α-helix	1320-1326	7
α-helix	1336-1346	11
α-helix	1354-1364	11
α-helix	1366-1368	3
α-helix	1374-1385	12
α-helix	1390-1403	14
α-helix	1410-1423	14
α-helix	1658	1
α-helix	1659-1664	6
α-helix	1665-1681	17
α-helix	1693-1703	11
α-helix	1705-1708	4
α-helix	1714-1725	12
α-helix	1729-1742	14
α-helix	1755-1777	23
α-helix	1781-1783	3
α-helix	1784-1798	15
α-helix	1802-1816	15
α-helix	1822-1834	13

1 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
Protein argonaute-2	A	protein	870	Homo sapiens	Q9UKV8 (AlphaFold model)
Elongin-B	B, C	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	D, E	protein	112	Homo sapiens	Q15369 (AlphaFold model)
miR-7	G	RNA	24	Homo sapiens
Cullin-3	H, I	protein	396	Homo sapiens	Q13618 (AlphaFold model)
CYRANO trigger RNA	T	RNA	120	Homo sapiens
Zinc finger SWIM domain-containing protein 8	M, N	protein	1866	Homo sapiens	A7E2V4

Sequence of entity 1 (A), FASTA

>9RWZ_1 Protein argonaute-2 (chains A)
MGSSHHHHHHGSYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDI
PKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIG
RDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHL
PSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQP
VIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPA
SHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAG
QRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVT
GRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKS
FTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVY
AEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQ
PVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVREL
LIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQK
RHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLW
DDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSH
TSGQSNGRDHQALAKAVQVHQDTLRTMYFA

Sequence of entity 2 (B, C), FASTA

>9RWZ_2 Elongin-B (chains B, C)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (D, E), FASTA

>9RWZ_3 Elongin-C (chains D, E)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (G), FASTA

>9RWZ_4 miR-7 (chains G)
UGGAAGACUAGUGAUUUUGUUGUU

Sequence of entity 5 (H, I), FASTA

>9RWZ_5 Cullin-3 (chains H, I)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLENLYFQ

Sequence of entity 6 (T), FASTA

>9RWZ_6 CYRANO trigger RNA (chains T)
GGGACAAAUGUUACAAGUUGUUUAAGAACAACAAAAUCACCAAUGUCUUCCAUUUUGAGA
UGUGUAUAGUUUUGUAAGCAUUAGUGCUUGGUAGCAUAUUGUAGUGCCAUGUUAGAAAAA

Sequence of entity 7 (M, N), FASTA

>9RWZ_7 Zinc finger SWIM domain-containing protein 8 (chains M, N)
MELMFAEWEDGERFSFEDSDRFEEDSLCSFISEAESLCQNWRGWRKQSAGPNSPTGGGGG
GGSGGTRMRDGLVIPLVELSAKQVAFHIPFEVVEKVYPPVPEQLQLRIAFWSFPENEEDI
RLYSCLANGSADEFQRGDQLFRMRAVKDPLQIGFHLSATVVPPQMVPPKGAYNVAVMFDR
CRVTSCSCTCGAGAKWCTHVVALCLFRIHNASAVCLRAPVSESLSRLQRDQLQKFAQYLI
SELPQQILPTAQRLLDELLSSQSTAINTVCGAPDPTAGPSASDQSTWYLDESTLTDNIKK
TLHKFCGPSPVVFSDVNSMYLSSTEPPAAAEWACLLRPLRGREPEGVWNLLSIVREMFKR
RDSNAAPLLEILTDQCLTYEQITGWWYSVRTSASHSSASGHTGRSNGQSEVAAHACASMC
DEMVTLWRLAVLDPALSPQRRRELCTQLRQWQLKVIENVKRGQHKKTLERLFPGFRPAVE
ACYFNWEEAYPLPGVTYSGTDRKLALCWARALPSRPGASRSGGLEESRDRPRPLPTEPAV
RPKEPGTKRKGLGEGVPSSQRGPRRLSAEGGDKALHKMGPGGGKAKALGGAGSGSKGSAG
GGSKRRLSSEDSSLEPDLAEMSLDDSSLALGAEASTFGGFPESPPPCPLHGGSRGPSTFL
PEPPDTYEEDGGVYFSEGPEPPTASVGPPGLLPGDVCTQDDLPSTDESGNGLPKTKEAAP
AVGEEDDDYQAYYLNAQDGAGGEEEKAEGGAGEEHDLFAGLKPLEQESRMEVLFACAEAL
HAHGYSSEASRLTVELAQDLLANPPDLKVEPPPAKGKKNKVSTSRQTWVATNTLSKAAFL
LTVLSERPEHHNLAFRVGMFALELQRPPASTKALEVKLAYQESEVAALLKKIPLGPSEMS
TMRCRAEELREGTLCDYRPVLPLMLASFIFDVLCAPGSRPPSRNWNSETPGDEELGFEAA
VAALGMKTTVSEAEHPLLCEGTRREKGDLALALMITYKDDQAKLKKILDKLLDRESQTHK
PQTLSSFYSSSRPTTASQRSPSKHGGPSAPGALQPLTSGSAGPAQPGSVAGAGPGPTEGF
TEKNVPESSPHSPCEGLPSEAALTPRPEGKVPSRLALGSRGGYNGRGWGSPGRPKKKHTG
MASIDSSAPETTSDSSPTLSRRPLRGGWAPTSWGRGQDSDSISSSSSDSLGSSSSSGSRR
ASASGGARAKTVEVGRYKGRRPESHAPHVPNQPSEAAAHFYFELAKTVLIKAGGNSSTSI
FTHPSSSGGHQGPHRNLHLCAFEIGLYALGLHNFVSPNWLSRTYSSHVSWITGQAMEIGS
AALTILVECWDGHLTPPEVASLADRASRARDSNMVRAAAELALSCLPHAHALNPNEIQRA
LVQCKEQDNLMLEKACMAVEEAAKGGGVYPEVLFEVAHQWFWLYEQTAGGSSTAREGATS
CSASGIRAGGEAGRGMPEGRGGPGTEPVTVAAAAVTAAATVVPVISVGSSLYPGPGLGHG
HSPGLHPYTALQPHLPCSPQYLTHPAHPAHPMPHMPRPAVFPVPSSAYPQGVHPAFLGAQ
YPYSVTPPSLAATAVSFPVPSMAPITVHPYHTEPGLPLPTSVACELWGQGTVSSVHPAST
FPAIQGASLPALTTQPSPLVSGGFPPPEEETHSQPVNPHSLHHLHAAYRVGMLALEMLGR
RAHNDHPNNFSRSPPYTDDVKWLLGLAAKLGVNYVHQFCVGAAKGVLSPFVLQEIVMETL
QRLSPAHAHNHLRAPAFHQLVQRCQQAYMQYIHHRLIHLTPADYDDFVNAIRSARSAFCL
TPMGMMQFNDILQNLKRSKQTKELWQRVSLEMATFSPGWSHPQFEKGGGSGGGSGGSAWS
HPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation. Farnung, J., Slobodyanyuk, E., Wang, P.Y. et al. Nature (2026) 652:784-793. DOI 10.1038/s41586-026-10232-0 · PubMed

Other PDB entries of the same protein (UniProt Q9UKV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BF2 1.59 Å, MID domain of Ago2 bound to UMP
4Z4D 1.6 Å, Human Argonaute2 Bound to t1-G Target RNA
3LUC 1.69 Å, Crystal structure of MID domain from hAGO2
3LUK 1.7 Å, Crystal structure of MID domain from hAGO2
7C6B 1.7 Å, Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine…
9LSN 1.75 Å, hAGO2-MID in complex with a chemical modified uridine monophosphate
9BF0 1.78 Å, MID domain of human Argo2 bound to UTP
3LUJ 1.8 Å, Crystal structure of MID domain from hAGO2 in complex with UMP
4Z4E 1.8 Å, Human Argonaute2 Bound to t1-U Target RNA
9LMZ 1.8 Å, hAGO2-MID in complex with a chemical modified uridine monophosphate
4W5O 1.8 Å, The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing…
3LUG 1.85 Å, Crystal structure of MID domain from hAGO2 in complex with CMP

Browse structure collections

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