SAXSdb — 8fy1

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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） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1	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 21–180； 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） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1	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） Apoptosis regulator Bcl-2 × 1 （P10415） ;N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1	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

Apoptosis regulator Bcl-2

Homo sapiens

UniProt P10415

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-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–209； UniProt 1–207

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	8fy1
Deposition date deposition_date	2023-01-25
Last revision last_revision	2024-04-10
Structure title title	E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2)
Keywords keywords	ternary complex, 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.

8fy1__assembly_1__model_1

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

Download this curve (.dat)

8fy1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8fy1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.05 Å
Rg (electron density)	33.12 Å
Total Rg	33.35 Å
Atom count	4027
Residues	484
Excluded volume	71771 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8fy1__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 (5)

Entity 1 Entity 1 polymer

Description description	von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	20729.5 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	4027

MGSSHHHHHHSSGLVPRGSHMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	Apoptosis regulator Bcl-2
Molecular weight formula_weight	23005.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSMAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSMR

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-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide ;
Molecular weight formula_weight	1640.5 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	47.482 Å
Unit-cell length b length_b	94.593 Å
Unit-cell length c length_c	81.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.560 Å
Low-resolution limit resolution_low	80.500 Å
R factor r_factor	0.2156
R_work r_work	0.2122
R_free r_free	0.2500

E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2)

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

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Apoptosis regulator Bcl-2

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

8fy1__assembly_1__model_1

8fy1__assembly_1__model_1 | I(q)

8fy1__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 (5)

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

7. Citations (1)

E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2)

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

Apoptosis regulator Bcl-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8fy1__assembly_1__model_1

8fy1__assembly_1__model_1 | I(q)

8fy1__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 (5)

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

7. Citations (1)