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8bub

Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Cyclin-dependent kinase 12 × 1 （Q9NYV4） Cyclin-K × 1 （O75909） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Cyclin-dependent kinase 12 × 1 （Q9NYV4） Cyclin-K × 1 （O75909） CITRIC ACID × 3 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Cyclin-dependent kinase 12 × 1 （Q9NYV4） Cyclin-K × 1 （O75909） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3e0c 8zsw 9bbe 9bbg 9bbh 9bbi 9ejq 9zxm 9zxn

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10ay 2hye 3ei1 3ei2 3ei3 3ei4 3ei4 3ei4 3i7h 3i7k 3i7l 3i7n

282 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–399； UniProt 1–395 Author chain A； PDBConstruct 409–840； UniProt 709–1140 Author chain D； PDBConstruct 5–399； UniProt 1–395 Author chain D； PDBConstruct 409–840； UniProt 709–1140 Author chain G； PDBConstruct 5–399； UniProt 1–395 Author chain G； PDBConstruct 409–840； UniProt 709–1140

Cyclin-dependent kinase 12

Homo sapiens

UniProt Q9NYV4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-K × 1 （O75909） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-K × 1 （O75909） CITRIC ACID × 3 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-K × 1 （O75909） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4nst 4nst

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4cxa 4cxa 4un0 4un0 5acb 5acb 6b3e 6b3e 6ckx 6ckx 6td3 6td3

103 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CDK12_HUMAN
Isoform Q9NYV4-3
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–343； UniProt 712–1051 Author chain E； PDBConstruct 4–343； UniProt 712–1051 Author chain H； PDBConstruct 4–343； UniProt 712–1051

Cyclin-K

Homo sapiens

UniProt O75909

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-dependent kinase 12 × 1 （Q9NYV4） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-dependent kinase 12 × 1 （Q9NYV4） CITRIC ACID × 3 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Cyclin-dependent kinase 12 × 1 （Q9NYV4） CITRIC ACID × 2 ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2i53 4nst 4nst

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4cxa 4cxa 4un0 4un0 5efq 5efq 6b3e 6b3e 6ckx 6ckx 6td3 6td3

105 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CCNK_HUMAN
Isoform O75909-4
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 5–271； UniProt 1–267 Author chain F； PDBConstruct 5–271； UniProt 1–267 Author chain I； PDBConstruct 5–271； UniProt 1–267

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_id8bub
Deposition date deposition_date2022-11-30
Structure title titleStructure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K
Keywords keywordskinase, cyclin, ubiquitin, degrader, LIGASE; LIGASE
Experimental Method methodX-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.

8bub__assembly_1__model_1

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

Download this curve (.dat)

8bub__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8bub__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）38.55 Å
Rg (electron density)38.16 Å
Total Rg38.52 Å
Atom count22461
Residues1400
Excluded volume201370 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8bub__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8bub__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 8bub__assembly_3__model_1 trimeric （3） 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 (5)

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id8bubA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubA02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id8bubB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id8bubB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id8bubD01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubD02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id8bubE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id8bubE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id8bubG01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubG02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8bubG03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id8bubH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id8bubH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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7. Citations (1)