7b5m

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2

Method: ELECTRON MICROSCOPY

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

Cullin-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–776； UniProt 1–776

E3 ubiquitin-protein ligase ARIH1

Homo sapiens

UniProt Q9Y4X5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARI1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–557； UniProt 1–557

S-phase kinase-associated protein 2

Homo sapiens

UniProt Q13309

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKP2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain T； PDBConstruct 1–424； UniProt 1–424

Cyclin-dependent kinases regulatory subunit 1

Homo sapiens

UniProt P61024

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CKS1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–79； UniProt 1–79

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKP1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain S； PDBConstruct 1–163； UniProt 1–163

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain U； PDBConstruct 1–75； UniProt 1–75

E3 ubiquitin-protein ligase RBX1

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBX1_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain R； PDBConstruct 1–108； UniProt 1–108

Cyclin-dependent kinase inhibitor 1B

Homo sapiens

UniProt P46527

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase ARIH1 × 1 （Q9Y4X5） S-phase kinase-associated protein 2 × 1 （Q13309） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-C × 1 （P0CG48） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDN1B_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–198； UniProt 1–198

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	7b5m
Deposition date deposition_date	2020-12-05
Structure title title	Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2
Keywords keywords	;ubiquitin, ubiquitin ligase, E3 ligase, F-box protein, RBR ligase, Cullin-RING-Ligase, CRL, SCF, NEDD8, Post-translational modification, ubiquitylation, 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.

7b5m__assembly_1__model_1

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

Download this curve (.dat)

7b5m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b5m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.35 Å
Rg (electron density)	53.56 Å
Total Rg	53.67 Å
Atom count	12530
Residues	1559
Excluded volume	223020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b5m__assembly_1__model_1`	octameric （8）	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 (9)

Entity 1 Entity 1 polymer

Description description	Cullin-1
Molecular weight formula_weight	89800.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	12530

MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase ARIH1
Molecular weight formula_weight	64005.6 kDa
EC 编号 ec_number	2.3.2.31
Mutation mutation	F430A, E431A, E503A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDGLLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSSAQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNRYMNHMQSLRAAHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATAVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLWEYIED

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 3 Entity 3 polymer

Description description	S-phase kinase-associated protein 2
Molecular weight formula_weight	47817.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQKPSCL

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 4 Entity 4 polymer

Description description	Cyclin-dependent kinases regulatory subunit 1
Molecular weight formula_weight	9679.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFRRPLPKKPKK

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 5 Entity 5 polymer

Description description	S-phase kinase-associated protein 1
Molecular weight formula_weight	18680.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

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	Polyubiquitin-C
Molecular weight formula_weight	8519.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG

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 7 Entity 7 polymer

Description description	E3 ubiquitin-protein ligase RBX1
Molecular weight formula_weight	12290.0 kDa
EC 编号 ec_number	2.3.2.27,2.3.2.32
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 8 Entity 8 polymer

Description description	Cyclin-dependent kinase inhibitor 1B
Molecular weight formula_weight	22185.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIGAPANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTSNKRANRTEENVSDGSPNAGSVEQTPRRPGLRRRQT

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	synthetic construct

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7b5mC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	7b5mU01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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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	3.91 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	759489

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2

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

Cullin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 ubiquitin-protein ligase ARIH1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

S-phase kinase-associated protein 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

Cyclin-dependent kinases regulatory subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

S-phase kinase-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-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

E3 ubiquitin-protein ligase RBX1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-dependent kinase inhibitor 1B

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

7b5m__assembly_1__model_1

7b5m__assembly_1__model_1 | I(q)

7b5m__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer