SAXSdb — 1lm8

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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） Hypoxia-inducible factor 1 alpha × 1 （Q16665） 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	1
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	ELONGIN B × 1 （Q15370） Von Hippel-Lindau disease tumor suppressor × 1 （P40337） Hypoxia-inducible factor 1 alpha × 1 （Q16665） 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	2
Chains and sequence ranges	Author chain C； 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） Hypoxia-inducible factor 1 alpha × 1 （Q16665） 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	3
Chains and sequence ranges	Author chain V； PDBConstruct 1–160； UniProt 54–213

Hypoxia-inducible factor 1 alpha

OrganismNot specified

UniProt Q16665

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） Von Hippel-Lindau disease tumor suppressor × 1 （P40337） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIF1A_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–20； UniProt 556–575

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	1lm8
Deposition date deposition_date	2002-04-30
Structure title title	Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
Keywords keywords	REGULATION, tumor suppressor, oxygen sensing, 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.

1lm8__assembly_1__model_1

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

Download this curve (.dat)

1lm8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lm8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	24.51 Å
Total Rg	25.23 Å
Atom count	2883
Residues	358
Excluded volume	51458 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lm8__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	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
Atom count atom_count	3406

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 2 Entity 2 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 3 Entity 3 polymer

Description description	Von Hippel-Lindau disease tumor suppressor
Molecular weight formula_weight	18558.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	Hypoxia-inducible factor 1 alpha
Molecular weight formula_weight	2427.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DLDLEMLAPYIPMDDDFQLR

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	523

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1lm8b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d1lm8c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d1lm8v_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.3 — VHL
Family Family family	b.3.3.1 — VHL

CATH v4.4 (4 domains)

Domain ID domain_id	1lm8B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	1lm8C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	1lm8V01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily	10 — von Hippel-Lindau disease tumour suppressor, alpha domain

Domain ID domain_id	1lm8V02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	780 — von Hippel-Lindau disease tumour suppressor, beta domain

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Unit-cell length a length_a	59.500 Å
Unit-cell length b length_b	59.500 Å
Unit-cell length c length_c	245.400 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2360

Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

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

Hypoxia-inducible factor 1 alpha

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

1lm8__assembly_1__model_1

1lm8__assembly_1__model_1 | I(q)

1lm8__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

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)