SAXSdb — 8ql1

▼

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

Notchless protein homolog 1

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 10–104	Not recorded	NDE1 × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium sulfate, 18.2% v/v Polyethylene glycol 300, 0.1 M Sodium Acetate, 3.5 M Ammonium chloride	Resolution 2.30 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 10–104	Not recorded	NDE1 × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium sulfate, 18.2% v/v Polyethylene glycol 300, 0.1 M Sodium Acetate, 3.5 M Ammonium chloride	Resolution 2.30 Å R-free 0.248
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 10–104	Not recorded	NDE1 × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium sulfate, 18.2% v/v Polyethylene glycol 300, 0.1 M Sodium Acetate, 3.5 M Ammonium chloride	Resolution 2.30 Å R-free 0.248
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 10–104	Not recorded	NDE1 × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Ammonium sulfate, 18.2% v/v Polyethylene glycol 300, 0.1 M Sodium Acetate, 3.5 M Ammonium chloride	Resolution 2.30 Å R-free 0.248

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 8QL1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8FL0 Human nucleolar pre-60S ribosomal subunit (State H) Deposited 2022-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain NJ 1–485（485 aa）	Not recorded	MG MAGNESIUM ION × 22 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.91 Å
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 65-meric	Chain NJ 1–485（485 aa）	Not recorded	MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.67 Å
8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 63-meric	Chain NJ 1–485（485 aa）	Not recorded	MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.53 Å
8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric	Chain NJ 1–485（485 aa）	Not recorded	MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.89 Å
8INK human nuclear pre-60S ribosomal particle - State D Deposited 2023-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain W 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8IPD human nuclear pre-60S ribosomal particle - State C Deposited 2023-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric	Chain W 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8IPX human nuclear pre-60S ribosomal particle - State C' Deposited 2023-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric	Chain W 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8IPY human nuclear pre-60S ribosomal particle - State D' Deposited 2023-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain W 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8IR1 human nuclear pre-60S ribosomal particle - State A Deposited 2023-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain N 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8IR3 human nuclear pre-60S ribosomal particle - State B' Deposited 2023-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric	Chain N 1–485（485 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8RL2 Human pre-60S - State 5 Deposited 2024-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric	Chain CG 1–485（485 aa）	Mutation：E85A	ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
9QIW Human pre-60S - State 3 Deposited 2025-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric	Chain CG 1–485（485 aa）	Mutation：E85A	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLE1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 9–103； UniProt 10–104 Author chain D； PDBConstruct 9–103； UniProt 10–104 Author chain F； PDBConstruct 9–103； UniProt 10–104 Author chain H； PDBConstruct 9–103； UniProt 10–104

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	8ql1
Deposition date deposition_date	2023-09-19
Structure title title	Crystal structure of the human MDN1-MIDAS/NLE1-UBL complex
Keywords keywords	AAA+ ATPase, Metal ion dependent adhesion site (MIDAS), Ubiquitin-like domain (Ubl), pre-60S biogenesis, RIBOSOME; RIBOSOME
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	40.25 Å
Radius of gyration Rg (electron density) rg_electron	39.88 Å
Forward intensity I(0) i0	302486000.00
Molecular weight molecular_weight	146970.0 kDa
Excluded volume excluded_volume	186210 Å³
Envelope volume envelope_volume	247140 Å³
Hydration-shell volume shell_volume	53100 Å³
Envelope diameter envelope_diameter	152.5 Å
Shell Rg shell_rg	44.07 Å
Envelope Rg envelope_rg	39.73 Å
Shape Rg shape_rg	39.88 Å
Total Rg total_rg	40.10 Å
Total atoms total_atoms	10355
Residues n_residues	1315
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	136.8 Å
Rg (real space) rg_real	40.29 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	3.0250e+08
I(0) uncertainty (real space) i0_real_error	5.1430e+06
Rg (reciprocal space) rg_reciprocal	40.25 Å
I(0) (reciprocal space) i0_reciprocal	302500000.0000
Solution quality estimate total_estimate	0.8071
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.6 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	70360000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NDE1
Molecular weight formula_weight	31598.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	10770

ELERQLEMWQPRESGNPEEEKVAAEMWQSYLILTAPLSQRLCEELRLILEGSGKPSKRQYQICLAIDDSSSMVDNHTKQLAFESLAVIGNALTLLEVGQIAVCSFGESVKLLHPFHEQFSDYSGSQILRLCKFQQKKTKIAQFLESVANMFAAAQQLSQNISSETAQLLLVVSDGRGLFLEGKERVLAAVQAARNANIFVIFVVLDNPSSRDSILDIKVPIFKGPGEMPEIRSYMEEFPFPYYIILRDVNALPETLSDALRQWFELVTASDHPHHHHHH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Notchless protein homolog 1
Molecular weight formula_weight	11497.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

HHHHHHGSVARDVQRLLVQFQDEGGQLLGSPFDVPVDITPDRLQLVCNALLAQEDPLPLAFFVHDAEIVSSLGKTLESQAVETEKVLDIIYQPQAIFRVRAVT

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	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	415

▶

8. Citations (1)

▶

Unit-cell length a length_a	237.160 Å
Unit-cell length b length_b	69.818 Å
Unit-cell length c length_c	103.183 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	118.520 Å
R factor r_factor	0.2161
R_work r_work	0.2144
R_free r_free	0.2476

fit	/app/data/saxs_computation/ql/8ql1/8ql1.fit
pddf	/app/data/pr_computation/ql/8ql1/8ql1.pr.out
profile	/app/data/saxs_computation/ql/8ql1/8ql1.dat

Crystal structure of the human MDN1-MIDAS/NLE1-UBL complex

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

Notchless protein homolog 1

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)