SAXSdb — 4a0l

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

DNA DAMAGE-BINDING PROTEIN 1

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） CULLIN-4B × 1 （Q13620） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） CULLIN-4B × 1 （Q13620） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–1144； UniProt 1–1140 Author chain C； PDBConstruct 5–1144； UniProt 1–1140

DNA DAMAGE-BINDING PROTEIN 2

DANIO RERIO

UniProt Q2YDS1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） CULLIN-4B × 1 （Q13620） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） CULLIN-4B × 1 （Q13620） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDB2_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 19–382； UniProt 60–423 Author chain D； PDBConstruct 19–382； UniProt 60–423

CULLIN-4B

HOMO SAPIENS

UniProt Q13620

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 （P62878） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL4B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 5–726； UniProt 192–913 Author chain H； PDBConstruct 5–726； UniProt 192–913

E3 UBIQUITIN-PROTEIN LIGASE RBX1

MUS MUSCULUS

UniProt P62878

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） CULLIN-4B × 1 （Q13620） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 4 DNA 2	DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） DNA DAMAGE-BINDING PROTEIN 2 × 1 （Q2YDS1） CULLIN-4B × 1 （Q13620） 12 BP THF CONTAINING DNA DUPLEX × 1 12 BP DNA DUPLEX × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBX1_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 2–98； UniProt 12–108 Author chain I； PDBConstruct 2–98； UniProt 12–108

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	4a0l
Deposition date deposition_date	2011-09-09
Structure title title	Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex
Keywords keywords	LIGASE-DNA-BINDING PROTEIN-DNA COMPLEX; LIGASE/DNA-BINDING PROTEIN/DNA
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.

4a0l__assembly_1__model_1

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

Download this curve (.dat)

4a0l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4a0l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.48 Å
Rg (electron density)	53.30 Å
Total Rg	53.46 Å
Atom count	17737
Residues	2213
Excluded volume	315310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4a0l__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4a0l__assembly_2__model_1`	hexameric （6）	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	DNA DAMAGE-BINDING PROTEIN 1
Molecular weight formula_weight	127425.8 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	35553

GGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

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	DNA DAMAGE-BINDING PROTEIN 2
Molecular weight formula_weight	43418.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MHHHHHHRRLVPRGSGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLKSYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAITGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATGDSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKNSYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLTPIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFSPTGDVLASGMGFNILIWNREDT

Source Source

Source organism organism	DANIO RERIO
Common name common_name	ZEBRAFISH
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	TRICHOPLUSIA NI

Entity 3 Entity 3 polymer

Description description	CULLIN-4B
Molecular weight formula_weight	84992.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGGRGSAKKLVIKNFKDKPKLPENYTDETWQKLKEAVEAIQNSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAIDRSLLRSLLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIKAFGSTIVINPEKDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEAFETFINKRPNKPAELIAKYVDSKLRAGNKEATDEELEKMLDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMIQFKQYMQNQNVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRKLQWQSTLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQSLACGKARVLAKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLKFPVKPADLKKRIESLIDRDYMERDKENPNQYNYIA

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 4 Entity 4 polymer

Description description	E3 UBIQUITIN-PROTEIN LIGASE RBX1
Molecular weight formula_weight	11330.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	HOUSE MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	TRICHOPLUSIA NI

Entity 5 Entity 5 polymer

Description description	12 BP THF CONTAINING DNA DUPLEX
Molecular weight formula_weight	3498.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R,T

GCTACTNACGCA

Entity 6 Entity 6 polymer

Description description	12 BP DNA DUPLEX
Molecular weight formula_weight	3702.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	S,U

TGCGTAAGTAGC

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Unit-cell length a length_a	130.800 Å
Unit-cell length b length_b	155.840 Å
Unit-cell length c length_c	255.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	7.400 Å
Low-resolution limit resolution_low	29.862 Å
R factor r_factor	0.3180
R_work r_work	0.3178
R_free r_free	0.3199

Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex

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

DNA DAMAGE-BINDING 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

DNA DAMAGE-BINDING 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

CULLIN-4B

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4a0l__assembly_1__model_1

4a0l__assembly_1__model_1 | I(q)

4a0l__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 (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

Entity 6 Entity 6 polymer

Polymer Polymer

7. Citations (1)