8vl9

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue

Method: X-RAY DIFFRACTION

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

von Hippel-Lindau disease tumor suppressor

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	Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Cysteine dioxygenase type 1 × 1 （Q16878） N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CITRIC ACID × 1 FE (II) ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VHL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–162； UniProt 54–213

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-C × 1 （Q15369） Cysteine dioxygenase type 1 × 1 （Q16878） N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CITRIC ACID × 1 FE (II) ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） Cysteine dioxygenase type 1 × 1 （Q16878） N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CITRIC ACID × 1 FE (II) ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–96； UniProt 17–112

Cysteine dioxygenase type 1

Homo sapiens

UniProt Q16878

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	von Hippel-Lindau disease tumor suppressor × 1 （P40337） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CITRIC ACID × 1 FE (II) ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDO1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–201； UniProt 1–200

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	8vl9
Deposition date deposition_date	2024-01-11
Structure title title	Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue
Keywords keywords	VHL, CDO1, VHL-small molecule-CDO1 ternary complex, degradation, APOPTOSIS; APOPTOSIS
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.

8vl9__assembly_1__model_1

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

Download this curve (.dat)

8vl9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vl9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.74 Å
Rg (electron density)	30.08 Å
Total Rg	30.75 Å
Atom count	4346
Residues	533
Excluded volume	77219 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vl9__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	18712.3 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	4466

GPMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	Elongin-B
Molecular weight formula_weight	13147.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

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	Elongin-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

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	Cysteine dioxygenase type 1
Molecular weight formula_weight	23061.0 kDa
EC 编号 ec_number	1.13.11.20
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GMEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSIGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN

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 non-polymer

Description description	N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide
Molecular weight formula_weight	491.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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Unit-cell length a length_a	116.657 Å
Unit-cell length b length_b	177.873 Å
Unit-cell length c length_c	103.824 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	48.774 Å
R factor r_factor	0.1855
R_work r_work	0.1840
R_free r_free	0.2160

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue

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

von Hippel-Lindau disease tumor suppressor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-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

Cysteine dioxygenase type 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8vl9__assembly_1__model_1

8vl9__assembly_1__model_1 | I(q)

8vl9__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)