SAXSdb — 4ajy

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

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2

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	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） HYPOXIA-INDUCIBLE FACTOR 1-ALPHA × 1 （Q16665） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） GLYCEROL × 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	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1

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	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） HYPOXIA-INDUCIBLE FACTOR 1-ALPHA × 1 （Q16665） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） GLYCEROL × 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–97； UniProt 1–96

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	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） GLYCEROL × 1 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	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–19； UniProt 559–577

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	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） HYPOXIA-INDUCIBLE FACTOR 1-ALPHA × 1 （Q16665） GLYCEROL × 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	4
Chains and sequence ranges	Author chain V； PDBConstruct 4–163； UniProt 214–373

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	4ajy
Deposition date deposition_date	2012-02-21
Structure title title	von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
Keywords keywords	E3 UBIQUITIN LIGASE, TRANSCRIPTION FACTOR, HYPOXIC SIGNALING, 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.

4ajy__assembly_1__model_1

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

Download this curve (.dat)

4ajy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ajy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.89 Å
Rg (electron density)	24.03 Å
Total Rg	24.71 Å
Atom count	2806
Residues	355
Excluded volume	50166 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ajy__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 (6)

Entity 1 Entity 1 polymer

Description description	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
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	3060

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	TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
Molecular weight formula_weight	10974.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

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	HYPOXIA-INDUCIBLE FACTOR 1-ALPHA
Molecular weight formula_weight	2260.5 kDa
Mutation mutation	YES
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DEALAPYIPMDDDFQLRSF

Entity 4 Entity 4 polymer

Description description	VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
Molecular weight formula_weight	18840.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

GSHMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	242

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4ajyB00
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	4ajyC00
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	4ajyV01
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

Domain ID domain_id	4ajyV02
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

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Unit-cell length a length_a	59.232 Å
Unit-cell length b length_b	59.232 Å
Unit-cell length c length_c	244.038 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	1.730 Å
Low-resolution limit resolution_low	42.500 Å
R factor r_factor	0.1924
R_work r_work	0.1903
R_free r_free	0.2324

von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide

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

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 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

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 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

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

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

4ajy__assembly_1__model_1

4ajy__assembly_1__model_1 | I(q)

4ajy__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 (6)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)