9rwz

ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein argonaute-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 2	Elongin-B × 2 （Q15370） Elongin-C × 2 （Q15369） miR-7 × 1 Cullin-3 × 2 （Q13618） CYRANO trigger RNA × 1 Zinc finger SWIM domain-containing protein 8 × 2 （A7E2V4） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGO2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–870； UniProt 2–859

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 2	Protein argonaute-2 × 1 （Q9UKV8） Elongin-C × 2 （Q15369） miR-7 × 1 Cullin-3 × 2 （Q13618） CYRANO trigger RNA × 1 Zinc finger SWIM domain-containing protein 8 × 2 （A7E2V4） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118 Author chain C； PDBConstruct 1–118； UniProt 1–118

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 2	Protein argonaute-2 × 1 （Q9UKV8） Elongin-B × 2 （Q15370） miR-7 × 1 Cullin-3 × 2 （Q13618） CYRANO trigger RNA × 1 Zinc finger SWIM domain-containing protein 8 × 2 （A7E2V4） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–112； UniProt 1–112 Author chain E； PDBConstruct 1–112； UniProt 1–112

Cullin-3

Homo sapiens

UniProt Q13618

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 2	Protein argonaute-2 × 1 （Q9UKV8） Elongin-B × 2 （Q15370） Elongin-C × 2 （Q15369） miR-7 × 1 CYRANO trigger RNA × 1 Zinc finger SWIM domain-containing protein 8 × 2 （A7E2V4） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 1–390； UniProt 1–390 Author chain I； PDBConstruct 1–390； UniProt 1–390

Zinc finger SWIM domain-containing protein 8

Homo sapiens

UniProt A7E2V4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 2	Protein argonaute-2 × 1 （Q9UKV8） Elongin-B × 2 （Q15370） Elongin-C × 2 （Q15369） miR-7 × 1 Cullin-3 × 2 （Q13618） CYRANO trigger RNA × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZSWM8_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain M； PDBConstruct 1–1837； UniProt 1–1837 Author chain N； PDBConstruct 1–1837； UniProt 1–1837

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rwz
Deposition date deposition_date	2025-07-10
Structure title title	ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
Keywords keywords	miRNA, E3 Ligase, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9rwz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9rwz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rwz__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	68.28 Å
Rg (electron density)	68.22 Å
Total Rg	67.92 Å
Atom count	28601
Residues	3659
Excluded volume	502880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rwz__assembly_1__model_1`	11-meric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Protein argonaute-2
Molecular weight formula_weight	98554.4 kDa
EC 编号 ec_number	3.1.26.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	28601

MGSSHHHHHHGSYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 Entity 2 polymer

Description description	Elongin-B
Molecular weight formula_weight	13147.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 3 Entity 3 polymer

Description description	Elongin-C
Molecular weight formula_weight	12485.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 4 Entity 4 polymer

Description description	miR-7
Molecular weight formula_weight	7690.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

UGGAAGACUAGUGAUUUUGUUGUU

Entity 5 Entity 5 polymer

Description description	Cullin-3
Molecular weight formula_weight	46410.1 kDa
Mutation mutation	I342R, L346D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I

MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRNAYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDRGAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLNLNSRSPEYLSLENLYFQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	CYRANO trigger RNA
Molecular weight formula_weight	38577.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	T

GGGACAAAUGUUACAAGUUGUUUAAGAACAACAAAAUCACCAAUGUCUUCCAUUUUGAGAUGUGUAUAGUUUUGUAAGCAUUAGUGCUUGGUAGCAUAUUGUAGUGCCAUGUUAGAAAAA

Entity 7 Entity 7 polymer

Description description	Zinc finger SWIM domain-containing protein 8
Molecular weight formula_weight	200458.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,M

MELMFAEWEDGERFSFEDSDRFEEDSLCSFISEAESLCQNWRGWRKQSAGPNSPTGGGGGGGSGGTRMRDGLVIPLVELSAKQVAFHIPFEVVEKVYPPVPEQLQLRIAFWSFPENEEDIRLYSCLANGSADEFQRGDQLFRMRAVKDPLQIGFHLSATVVPPQMVPPKGAYNVAVMFDRCRVTSCSCTCGAGAKWCTHVVALCLFRIHNASAVCLRAPVSESLSRLQRDQLQKFAQYLISELPQQILPTAQRLLDELLSSQSTAINTVCGAPDPTAGPSASDQSTWYLDESTLTDNIKKTLHKFCGPSPVVFSDVNSMYLSSTEPPAAAEWACLLRPLRGREPEGVWNLLSIVREMFKRRDSNAAPLLEILTDQCLTYEQITGWWYSVRTSASHSSASGHTGRSNGQSEVAAHACASMCDEMVTLWRLAVLDPALSPQRRRELCTQLRQWQLKVIENVKRGQHKKTLERLFPGFRPAVEACYFNWEEAYPLPGVTYSGTDRKLALCWARALPSRPGASRSGGLEESRDRPRPLPTEPAVRPKEPGTKRKGLGEGVPSSQRGPRRLSAEGGDKALHKMGPGGGKAKALGGAGSGSKGSAGGGSKRRLSSEDSSLEPDLAEMSLDDSSLALGAEASTFGGFPESPPPCPLHGGSRGPSTFLPEPPDTYEEDGGVYFSEGPEPPTASVGPPGLLPGDVCTQDDLPSTDESGNGLPKTKEAAPAVGEEDDDYQAYYLNAQDGAGGEEEKAEGGAGEEHDLFAGLKPLEQESRMEVLFACAEALHAHGYSSEASRLTVELAQDLLANPPDLKVEPPPAKGKKNKVSTSRQTWVATNTLSKAAFLLTVLSERPEHHNLAFRVGMFALELQRPPASTKALEVKLAYQESEVAALLKKIPLGPSEMSTMRCRAEELREGTLCDYRPVLPLMLASFIFDVLCAPGSRPPSRNWNSETPGDEELGFEAAVAALGMKTTVSEAEHPLLCEGTRREKGDLALALMITYKDDQAKLKKILDKLLDRESQTHKPQTLSSFYSSSRPTTASQRSPSKHGGPSAPGALQPLTSGSAGPAQPGSVAGAGPGPTEGFTEKNVPESSPHSPCEGLPSEAALTPRPEGKVPSRLALGSRGGYNGRGWGSPGRPKKKHTGMASIDSSAPETTSDSSPTLSRRPLRGGWAPTSWGRGQDSDSISSSSSDSLGSSSSSGSRRASASGGARAKTVEVGRYKGRRPESHAPHVPNQPSEAAAHFYFELAKTVLIKAGGNSSTSIFTHPSSSGGHQGPHRNLHLCAFEIGLYALGLHNFVSPNWLSRTYSSHVSWITGQAMEIGSAALTILVECWDGHLTPPEVASLADRASRARDSNMVRAAAELALSCLPHAHALNPNEIQRALVQCKEQDNLMLEKACMAVEEAAKGGGVYPEVLFEVAHQWFWLYEQTAGGSSTAREGATSCSASGIRAGGEAGRGMPEGRGGPGTEPVTVAAAAVTAAATVVPVISVGSSLYPGPGLGHGHSPGLHPYTALQPHLPCSPQYLTHPAHPAHPMPHMPRPAVFPVPSSAYPQGVHPAFLGAQYPYSVTPPSLAATAVSFPVPSMAPITVHPYHTEPGLPLPTSVACELWGQGTVSSVHPASTFPAIQGASLPALTTQPSPLVSGGFPPPEEETHSQPVNPHSLHHLHAAYRVGMLALEMLGRRAHNDHPNNFSRSPPYTDDVKWLLGLAAKLGVNYVHQFCVGAAKGVLSPFVLQEIVMETLQRLSPAHAHNHLRAPAFHQLVQRCQQAYMQYIHHRLIHLTPADYDDFVNAIRSARSAFCLTPMGMMQFNDILQNLKRSKQTKELWQRVSLEMATFSPGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	230859

ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein argonaute-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cullin-3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Zinc finger SWIM domain-containing protein 8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9rwz__assembly_1__model_1

9rwz__assembly_1__model_1 | I(q)

9rwz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)