7b5l

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1

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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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 1–73； UniProt 1–73

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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEDD8_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–76； UniProt 1–76

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 12	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） NEDD8 × 1 （Q15843） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	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	8
Chains and sequence ranges	Author chain R； PDBConstruct 1–108； UniProt 1–108

Ubiquitin-conjugating enzyme E2 L3

Homo sapiens

UniProt P68036

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UB2L3_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain D； PDBConstruct 1–154； UniProt 1–154

Cyclin-dependent kinase 2

Homo sapiens

UniProt P24941

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-A2 × 1 （P20248） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK2_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain L； PDBConstruct 1–298； UniProt 1–298

Cyclin-A2

Homo sapiens

UniProt P20248

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-dependent kinase inhibitor 1B × 1 （P46527） ZINC ION × 9 5-azanylpentan-2-one × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNA2_HUMAN
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain Y； PDBConstruct 1–432； UniProt 1–432

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 12	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） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） Ubiquitin-conjugating enzyme E2 L3 × 1 （P68036） Cyclin-dependent kinase 2 × 1 （P24941） Cyclin-A2 × 1 （P20248） ZINC ION × 9 5-azanylpentan-2-one × 1	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	12
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	7b5l
Deposition date deposition_date	2020-12-04
Structure title title	Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1
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.

7b5l__assembly_1__model_1

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

Download this curve (.dat)

7b5l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b5l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.06 Å
Rg (electron density)	66.52 Å
Total Rg	66.48 Å
Atom count	21529
Residues	2652
Excluded volume	385160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b5l__assembly_1__model_1`	dodecameric （12）	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 (14)

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	21529

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	64197.8 kDa
EC 编号 ec_number	2.3.2.31
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDGLLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSSAQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLWEYIED

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	8968.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFRRPL

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	NEDD8
Molecular weight formula_weight	8574.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG

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 8 Entity 8 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 9 Entity 9 polymer

Description description	Ubiquitin-conjugating enzyme E2 L3
Molecular weight formula_weight	17825.5 kDa
EC 编号 ec_number	2.3.2.23
Mutation mutation	C17A, C137A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAASRRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD

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 10 Entity 10 polymer

Description description	Cyclin-dependent kinase 2
Molecular weight formula_weight	34056.5 kDa
EC 编号 ec_number	2.7.11.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

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 11 Entity 11 polymer

Description description	Cyclin-A2
Molecular weight formula_weight	48609.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRGLAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKIEREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIILEDEKPVSVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL

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 12 Entity 12 polymer

Description description	Cyclin-dependent kinase inhibitor 1B
Molecular weight formula_weight	22188.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIGAPANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPNAGSVEQTPKKPGLRRRQT

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 13 Entity 13 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 14 Entity 14 non-polymer

Description description	5-azanylpentan-2-one
Molecular weight formula_weight	101.1 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7b5lC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	7b5lL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	7b5lN01
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

Domain ID domain_id	7b5lU01
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

▶

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	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	623409

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1

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

NEDD8

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

Ubiquitin-conjugating enzyme E2 L3

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 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer