SAXSdb — 8caf

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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 4	Fab Light Chain × 1 Fab Heavy Chain × 1 NEDD8 × 1 （Q15843）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fab Light Chain × 1 Fab Heavy Chain × 1 NEDD8 × 1 （Q15843）	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	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–79； UniProt 698–776 Author chain H； PDBConstruct 1–79； UniProt 698–776

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 4	Fab Light Chain × 1 Fab Heavy Chain × 1 Cullin-1 × 1 （Q13616）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fab Light Chain × 1 Fab Heavy Chain × 1 Cullin-1 × 1 （Q13616）	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	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76

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	8caf
Deposition date deposition_date	2023-01-24
Structure title title	N8C_Fab3b in complex with NEDD8-CUL1(WHB)
Keywords keywords	NEDD8, Cullin-RING ligase, ubiquitin, antibody, CELL CYCLE; CELL CYCLE
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.

8caf__assembly_1__model_1

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

Download this curve (.dat)

8caf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8caf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.36 Å
Rg (electron density)	29.22 Å
Total Rg	29.92 Å
Atom count	4394
Residues	575
Excluded volume	78381 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8caf__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8caf__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Fab Light Chain
Molecular weight formula_weight	22958.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8808

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Fab Heavy Chain
Molecular weight formula_weight	23392.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSSYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARDPFGWAAHGVGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Cullin-1
Molecular weight formula_weight	9341.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

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 K-12

Entity 4 Entity 4 polymer

Description description	NEDD8
Molecular weight formula_weight	8574.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G

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 K-12

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	8cafA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8cafE01
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	8cafF01
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	8cafG01
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	8cafH01
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

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Unit-cell length a length_a	102.372 Å
Unit-cell length b length_b	106.871 Å
Unit-cell length c length_c	180.651 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.660 Å
Low-resolution limit resolution_low	90.330 Å
R factor r_factor	0.2189
R_work r_work	0.2166
R_free r_free	0.2630

N8C_Fab3b in complex with NEDD8-CUL1(WHB)

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

NEDD8

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8caf__assembly_1__model_1

8caf__assembly_1__model_1 | I(q)

8caf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

N8C_Fab3b in complex with NEDD8-CUL1(WHB)

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8caf__assembly_1__model_1

8caf__assembly_1__model_1 | I(q)

8caf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)