9bju

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

Method: X-RAY DIFFRACTION

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

Elongin-B

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-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 1 ACETATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 DIMETHYL SULFOXIDE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Elongin-C × 1 （Q15369） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 1,2-ETHANEDIOL × 1 DIMETHYL SULFOXIDE × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	Q15370-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain G； PDBConstruct 1–104； UniProt 1–104 Author chain J； PDBConstruct 1–104； UniProt 1–104

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	Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 1 ACETATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 DIMETHYL SULFOXIDE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） von Hippel-Lindau disease tumor suppressor × 1 （P40337） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 1,2-ETHANEDIOL × 1 DIMETHYL SULFOXIDE × 1 water × 3	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 17–112 Author chain E； PDBConstruct 1–96； UniProt 17–112 Author chain H； PDBConstruct 1–96； UniProt 17–112 Author chain K； PDBConstruct 1–96； UniProt 17–112

von Hippel-Lindau disease tumor suppressor

Homo sapiens

UniProt P40337

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） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 1 ACETATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 ACETATE ION × 1 DIMETHYL SULFOXIDE × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE × 1 trifluoroacetic acid × 1 1,2-ETHANEDIOL × 1 DIMETHYL SULFOXIDE × 1 water × 3	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	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 17–176； UniProt 54–213 Author chain L； PDBConstruct 17–176； UniProt 54–213 Author chain F； PDBConstruct 17–176； UniProt 54–213 Author chain I； PDBConstruct 17–176； UniProt 54–213

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	9bju
Deposition date deposition_date	2024-04-25
Structure title title	Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5
Keywords keywords	VHL, degradation, degrader, TRANSCRIPTION; TRANSCRIPTION
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.

9bju__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9bju__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bju__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	24.99 Å
Rg (electron density)	24.10 Å
Total Rg	24.79 Å
Atom count	2751
Residues	336
Excluded volume	49250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bju__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9bju__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9bju__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9bju__assembly_4__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 (11)

Entity 1 Entity 1 polymer

Description description	Elongin-B
Molecular weight formula_weight	11748.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	11148

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

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-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

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 3 Entity 3 polymer

Description description	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	20530.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,L

MHHHHHHGENLYFQGSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	20514.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MHHHHHHGENLYFQGSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
Molecular weight formula_weight	491.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,X,Y,Z

XVPXX

Entity 6 Entity 6 non-polymer

Description description	trifluoroacetic acid
Molecular weight formula_weight	114.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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Unit-cell length a length_a	93.297 Å
Unit-cell length b length_b	93.297 Å
Unit-cell length c length_c	362.757 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	32

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.470 Å
Low-resolution limit resolution_low	48.860 Å
R factor r_factor	0.2203
R_work r_work	0.2184
R_free r_free	0.2556

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9bju__assembly_3__model_1

9bju__assembly_3__model_1 | I(q)

9bju__assembly_3__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 (11)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)