SAXSdb — 8djk

▼

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

3-hydroxy-3-methylglutaryl-coenzyme A reductase

Cricetulus griseus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	UbiA prenyltransferase domain-containing protein 1 × 1 （G3IEF0） Soluble cytochrome b562 × 1 （P0ABE7） Fab 15B2 Light Chain × 1 Fab 15B2 Heavy Chain × 1 CHOLESTEROL HEMISUCCINATE × 6 Digitonin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMDH_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–364； UniProt 2–356

UbiA prenyltransferase domain-containing protein 1

Cricetulus griseus

UniProt G3IEF0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	3-hydroxy-3-methylglutaryl-coenzyme A reductase × 1 （P00347） Soluble cytochrome b562 × 1 （P0ABE7） Fab 15B2 Light Chain × 1 Fab 15B2 Heavy Chain × 1 CHOLESTEROL HEMISUCCINATE × 6 Digitonin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3IEF0_CRIGR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–301； UniProt 41–338

Soluble cytochrome b562

Escherichia coli

UniProt P0ABE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	3-hydroxy-3-methylglutaryl-coenzyme A reductase × 1 （P00347） UbiA prenyltransferase domain-containing protein 1 × 1 （G3IEF0） Fab 15B2 Light Chain × 1 Fab 15B2 Heavy Chain × 1 CHOLESTEROL HEMISUCCINATE × 6 Digitonin × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C562_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–108； UniProt 25–127

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8djk
Deposition date deposition_date	2022-06-30
Structure title title	HMGCR-UBIAD1 Complex State 2
Keywords keywords	Cholesterol, MEMBRANE PROTEIN, Oxidoreductase-Immune System complex; Oxidoreductase/Immune System
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8djk__assembly_1__model_1

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

Download this curve (.dat)

8djk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8djk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.74 Å
Rg (electron density)	32.89 Å
Total Rg	33.58 Å
Atom count	7091
Residues	870
Excluded volume	129180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8djk__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	3-hydroxy-3-methylglutaryl-coenzyme A reductase
Molecular weight formula_weight	41215.9 kDa
EC 编号 ec_number	1.1.1.34
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	7091

MDYKDDDDKLSRLFRMHGLFVASHPWEVIVGTVTLTICMMSMNMFTGNNKICGWNYECPKFEEDVLSSDIIILTITRCIAILYIYFQFQNLRQLGSRYILGIAGLFTIFSSFVFSTVVIHFLDKELTGLNEALPFFLLLIDLSRASALAKFALSSNSQDEVRENIARGMAILGPTFTLDALVECLVIGVGTMSGVRQLEIMCCFGCMSVLANYFVFMTFFPACVSLVLELSRESREGRPIWQLSHFARVLEEEENRPNPVTQRVKMIMSLGLVLVHAHSRWIADPSPQNSTTEHSKVSLGLDEDVSKRIEPSVSLWQFYLSKMISMDIEQVVTLSLAFLLAVKYIFFEQAETESTLSLKNPITS

Source Source

Source organism organism	Cricetulus griseus
Common name common_name	Chinese hamster
NCBI taxonomy ID ncbi_taxonomy_id	10029
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	UbiA prenyltransferase domain-containing protein 1
Molecular weight formula_weight	32780.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MASSWRQKCASYVLALRPWSFSASLTPVALGSALAYRSQGVLDPRLLVGCAVAVLAVHGAGNLVSTYYDFSKGIDHKKSDDRTLVDRILEPQDVVRFGVFLYTLGCVCAACLYYLSTLKLEHLALIYFGGLSGSFLYTGGIGFKYVALGDLIILITFGPLAVMFAYAVQVGSLAIFPLVYAIPLALSTEAILHSNNTRDMESDQEAGIVTLAILIGPTFSYVLYNTLLFLPYLIFSILATHCSISLALPLLTIPMAFSLERQFRSQAFNKLPQRTAKLNLLLGLFYVFGIILAPAGSLPRL

Source Source

Source organism organism	Cricetulus griseus
Common name common_name	Chinese hamster
NCBI taxonomy ID ncbi_taxonomy_id	10029
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Soluble cytochrome b562
Molecular weight formula_weight	13470.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ARRLALEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLQKEV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Fab 15B2 Light Chain
Molecular weight formula_weight	23373.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DILLTQSPAILSVSPGERVSFSCRASQSIGTSIHWYQQRTNGSPRLVIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNSWPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Fab 15B2 Heavy Chain
Molecular weight formula_weight	25175.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQQSGPELVKPGASVKMSCKASGYSFTGYFMNWVKQSHGKSLEWIGRINPYNGDTFYNQKFKGKATLTVDKSSRTAHMELRSLTSADSALYFCVRRGEDYGSSYNYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 non-polymer

Description description	CHOLESTEROL HEMISUCCINATE
Molecular weight formula_weight	486.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	Digitonin
Molecular weight formula_weight	1229.3 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8djkH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8djkL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.330 Å
Low-resolution limit resolution_low	269.440 Å
R factor r_factor	0.4873
R_work r_work	0.4873
R_free r_free	—

Resolution resolution	3.33 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	285496

HMGCR-UBIAD1 Complex State 2

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

3-hydroxy-3-methylglutaryl-coenzyme A reductase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UbiA prenyltransferase domain-containing protein 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

Soluble cytochrome b562

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

8djk__assembly_1__model_1

8djk__assembly_1__model_1 | I(q)

8djk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)