1ldk

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex

Method: X-RAY DIFFRACTION

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

CULLIN HOMOLOG

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	ring-box protein 1 × 1 （P62877） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 1 （P63208） SKP2-like protein type gamma × 1 （Q13309） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	ring-box protein 1 × 2 （P62877） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 2 （P63208） SKP2-like protein type gamma × 2 （Q13309） ZINC ION × 6	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, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–396； UniProt 15–410 Author chain B； PDBConstruct 1–366； UniProt 411–776

ring-box protein 1

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 5	CULLIN HOMOLOG × 1 （Q13616） CULLIN HOMOLOG × 1 （Q13616） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 1 （P63208） SKP2-like protein type gamma × 1 （Q13309） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	CULLIN HOMOLOG × 2 （Q13616） CULLIN HOMOLOG × 2 （Q13616） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 2 （P63208） SKP2-like protein type gamma × 2 （Q13309） ZINC ION × 6	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–90； UniProt 19–108

CYCLIN A/CDK2-ASSOCIATED PROTEIN P19

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 5	CULLIN HOMOLOG × 1 （Q13616） CULLIN HOMOLOG × 1 （Q13616） ring-box protein 1 × 1 （P62877） SKP2-like protein type gamma × 1 （Q13309） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	CULLIN HOMOLOG × 2 （Q13616） CULLIN HOMOLOG × 2 （Q13616） ring-box protein 1 × 2 （P62877） SKP2-like protein type gamma × 2 （Q13309） ZINC ION × 6	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–133； UniProt 1–139

SKP2-like protein type gamma

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 5	CULLIN HOMOLOG × 1 （Q13616） CULLIN HOMOLOG × 1 （Q13616） ring-box protein 1 × 1 （P62877） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 1 （P63208） ZINC ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	CULLIN HOMOLOG × 2 （Q13616） CULLIN HOMOLOG × 2 （Q13616） ring-box protein 1 × 2 （P62877） CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 × 2 （P63208） ZINC ION × 6	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	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–41； UniProt 97–137

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	1ldk
Deposition date deposition_date	2002-04-08
Structure title title	Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
Keywords keywords	SCF, cullin, rbx1, roc1, hrt1, skp1, skp2, F-box, fbox, ubiquitin, ubiquitination, E3 ligase, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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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.

1ldk__assembly_1__model_1

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

Download this curve (.dat)

1ldk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ldk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.49 Å
Rg (electron density)	53.18 Å
Total Rg	53.15 Å
Atom count	7922
Residues	971
Excluded volume	141900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ldk__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ldk__assembly_2__model_1`	decameric （10）	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 (6)

Entity 1 Entity 1 polymer

Description description	CULLIN HOMOLOG
Molecular weight formula_weight	45754.8 kDa
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	7922

IGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTK

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 2 Entity 2 polymer

Description description	CULLIN HOMOLOG
Molecular weight formula_weight	42507.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAQSSSKSPELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

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	ring-box protein 1
Molecular weight formula_weight	10655.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

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 A/CDK2-ASSOCIATED PROTEIN P19
Molecular weight formula_weight	15033.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

PSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFN

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	SKP2-like protein type gamma
Molecular weight formula_weight	4759.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

WDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLW

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ldka_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.17 — Cullin repeat-like
Family Family family	a.118.17.1 — Cullin repeat

Domain ID domain_id	d1ldkb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.34 — SCF ubiquitin ligase complex WHB domain

Domain ID domain_id	d1ldkb2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.40 — Cullin homology domain
Superfamily Superfamily superfamily	e.40.1 — Cullin homology domain
Family Family family	e.40.1.1 — Cullin homology domain

Domain ID domain_id	d1ldkc_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d1ldkd1
Class class	a — All alpha proteins
Fold Fold fold	a.157 — Skp1 dimerisation domain-like
Superfamily Superfamily superfamily	a.157.1 — Skp1 dimerisation domain-like
Family Family family	a.157.1.1 — Skp1 dimerisation domain-like

Domain ID domain_id	d1ldkd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d1ldke1
Class class	a — All alpha proteins
Fold Fold fold	a.158 — F-box domain
Superfamily Superfamily superfamily	a.158.1 — F-box domain
Family Family family	a.158.1.1 — F-box domain

CATH v4.4 (9 domains)

Domain ID domain_id	1ldkA01
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	1ldkA02
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	1ldkA03
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	1ldkB01
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	1ldkB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	130 — Cullin; Chain C, Domain 2

Domain ID domain_id	1ldkB03
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	1ldkC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	1ldkD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	1ldkE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	219.378 Å
Unit-cell length b length_b	50.529 Å
Unit-cell length c length_c	158.610 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2890
R_free r_free	0.3310

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex

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

CULLIN HOMOLOG

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ring-box 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

CYCLIN A/CDK2-ASSOCIATED PROTEIN P19

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SKP2-like protein type gamma

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

1ldk__assembly_1__model_1

1ldk__assembly_1__model_1 | I(q)

1ldk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

CATH v4.4 (9 domains)

7. Citations (1)