SAXSdb — 8w4j

▼

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

Glutamate dehydrogenase 1, mitochondrial

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–558 Chain B； UniProt 1–558 Chain C； UniProt 1–558 Chain D； UniProt 1–558 Chain E； UniProt 1–558 Chain F； UniProt 1–558	Not recorded	Kelch-like protein 22 × 2 （Q53GT1）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8W4J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L1F Structure of human glutamate dehydrogenase-apo form Deposited 2002-02-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 54–558（505 aa） Chain B 54–558（505 aa） Chain C 54–558（505 aa） Chain D 54–558（505 aa） Chain E 54–558（505 aa） Chain F 54–558（505 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 8000, NaCl, sodium phosphate, sodium azide, octyl-b-glucopyranoside, methyl pentanediol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.302
1NR1 Crystal structure of the R463A mutant of human Glutamate dehydrogenase Deposited 2003-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 63–558（496 aa） Chain B 63–558（496 aa） Chain C 63–558（496 aa） Chain D 63–558（496 aa） Chain E 63–558（496 aa） Chain F 63–558（496 aa）	Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；sodium phosphate, PEG 8000, BOG, sodium chloride, MPD, sodium azide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.30 Å R-free 0.284
6DQG Human glutamate dehydrogenase, H454Y mutant Deposited 2018-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 63–558（496 aa） Fragment：UNP residues 63-558 Chain B 63–558（496 aa） Fragment：UNP residues 63-558 Chain C 63–558（496 aa） Fragment：UNP residues 63-558 Chain D 63–558（496 aa） Fragment：UNP residues 63-558 Chain E 63–558（496 aa） Fragment：UNP residues 63-558 Chain F 63–558（496 aa） Fragment：UNP residues 63-558	Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y	PO4 PHOSPHATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；295 K；Reservoir: 10% w/v PEG8000, 0.1 M sodium chloride, 1.3% w/v octyl-b-glucopyranoside, 7.5% v/v MPD, 0.1 M sodium phosphate, pH 6.8, 1 mM sodium azide	Resolution 2.70 Å R-free 0.279
7UZM Glutamate dehydrogenase 1 from human liver Deposited 2022-05-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8KGY Human glutamate dehydrogenase I Deposited 2023-08-20	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 200 mM NaCl, 2 mM MgCl2 and 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
8SK8 human liver mitochondrial Glutamate dehydrogenase 1 Deposited 2023-04-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.31 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHE3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–558； UniProt 1–558 Author chain B； PDBConstruct 1–558； UniProt 1–558 Author chain C； PDBConstruct 1–558； UniProt 1–558 Author chain D； PDBConstruct 1–558； UniProt 1–558 Author chain E； PDBConstruct 1–558； UniProt 1–558 Author chain F； PDBConstruct 1–558； UniProt 1–558

Kelch-like protein 22

Homo sapiens

UniProt Q53GT1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain I； UniProt 1–634 Chain J； UniProt 1–634	Not recorded	Glutamate dehydrogenase 1, mitochondrial × 6 （P00367）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8W4J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8K8T Structure of CUL3-RBX1-KLHL22 complex Deposited 2023-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 1–634（634 aa） Chain L 1–634（634 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8K9I Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif Deposited 2023-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 1–178（178 aa） Chain L 1–178（178 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8KHP CULLIN3-KLHL22-RBX1 E3 ligase Deposited 2023-08-22	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–634（634 aa） Chain B 1–634（634 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLH22_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–634； UniProt 1–634 Author chain J； PDBConstruct 1–634； UniProt 1–634

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	8w4j
Deposition date deposition_date	2023-08-24
Structure title title	Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I
Keywords keywords	E3 ligase, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	55.66 Å
Radius of gyration Rg (electron density) rg_electron	54.68 Å
Forward intensity I(0) i0	2310800000.00
Molecular weight molecular_weight	384160.0 kDa
Excluded volume excluded_volume	472820 Å³
Envelope volume envelope_volume	795070 Å³
Hydration-shell volume shell_volume	118140 Å³
Envelope diameter envelope_diameter	203.9 Å
Shell Rg shell_rg	58.36 Å
Envelope Rg envelope_rg	56.88 Å
Shape Rg shape_rg	54.83 Å
Total Rg total_rg	54.29 Å
Total atoms total_atoms	27165
Residues n_residues	4059
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	196.1 Å
Rg (real space) rg_real	55.83 Å
Rg uncertainty (real space) rg_real_error	2.12 Å
I(0) (real space) i0_real	2.3110e+09
I(0) uncertainty (real space) i0_real_error	4.8030e+07
Rg (reciprocal space) rg_reciprocal	55.51 Å
I(0) (reciprocal space) i0_reciprocal	2310000000.0000
Solution quality estimate total_estimate	0.8299
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.0 Å
Skewness Skewness skewness	0.523
Kurtosis Kurtosis kurtosis	-0.066
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	286100000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.720

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Glutamate dehydrogenase 1, mitochondrial
Molecular weight formula_weight	61480.7 kDa
EC 编号 ec_number	1.4.1.3
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	27165

MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADREDDPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT

Entity 2 Entity 2 polymer

Description description	Kelch-like protein 22
Molecular weight formula_weight	71744.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAEEQEFTQLCKLPAQPSHPHCVNNTYRSAQHSQALLRGLLALRDSGILFDVVLVVEGRHIEAHRILLAASCDYFRGMFAGGLKEMEQEEVLIHGVSYNAMCQILHFIYTSELELSLSNVQETLVAACQLQIPEIIHFCCDFLMSWVDEENILDVYRLAELFDLSRLTEQLDTYILKNFVAFSRTDKYRQLPLEKVYSLLSSNRLEVSCETEVYEGALLYHYSLEQVQADQISLHEPPKLLETVRFPLMEAEVLQRLHDKLDPSPLRDTVASALMYHRNESLQPSLQSPQTELRSDFQCVVGFGGIHSTPSTVLSDQAKYLNPLLGEWKHFTASLAPRMSNQGIAVLNNFVYLIGGDNNVQGFRAESRCWRYDPRHNRWFQIQSLQQEHADLSVCVVGRYIYAVAGRDYHNDLNAVERYDPATNSWAYVAPLKREVYAHAGATLEGKMYITCGRRGEDYLKETHCYDPGSNTWHTLADGPVRRAWHGMATLLNKLYVIGGSNNDAGYRRDVHQVACYSCTSGQWSSVCPLPAGHGEPGIAVLDNRIYVLGGRSHNRGSRTGYVHIYDVEKDCWEEGPQLDNSISGLAACVLTLPRSLLLEPPRGTPDRSQADPDFASEVMSVSDWEEFDNSSED

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

▶

8. Citations (1)

▶

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	3.06 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	62817

fit	/app/data/saxs_computation/w4/8w4j/8w4j.fit
pddf	/app/data/pr_computation/w4/8w4j/8w4j.pr.out
profile	/app/data/saxs_computation/w4/8w4j/8w4j.dat

Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I

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

Glutamate dehydrogenase 1, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Kelch-like protein 22

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)