SAXSdb — 9x5u

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

Urea-proton symporter DUR3

Arabidopsis thaliana

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–704 Chain B； UniProt 1–704 Chain C； UniProt 1–704 Chain D； UniProt 1–704	Not recorded	URE UREA × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.19 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 9X5U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9J7C Arabidopsis high-affinity urea transport DUR3 in the urea-bound occluded conformation, dimeric state Deposited 2024-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–704（704 aa） Chain B 1–704（704 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 4 URE UREA × 2 R16 HEXADECANE × 2 C14 TETRADECANE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9J7D Arabidopsis high-affinity urea transport DUR3 in the inward-facing open conformation, dimeric state Deposited 2024-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–704（704 aa） Chain B 1–704（704 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 4 C14 TETRADECANE × 1 R16 HEXADECANE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DUR3_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–704； UniProt 1–704 Author chain B； PDBConstruct 1–704； UniProt 1–704 Author chain C； PDBConstruct 1–704； UniProt 1–704 Author chain D； PDBConstruct 1–704； UniProt 1–704

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	9x5u
Deposition date deposition_date	2025-10-14
Structure title title	Arabidopsis thaliana URE transporter DUR3 - URE bound
Keywords keywords	URE transporter, homotetramer, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	50.22 Å
Radius of gyration Rg (electron density) rg_electron	49.50 Å
Forward intensity I(0) i0	1000240000.00
Molecular weight molecular_weight	286830.0 kDa
Excluded volume excluded_volume	368700 Å³
Envelope volume envelope_volume	544950 Å³
Hydration-shell volume shell_volume	90201 Å³
Envelope diameter envelope_diameter	161.5 Å
Shell Rg shell_rg	56.16 Å
Envelope Rg envelope_rg	47.14 Å
Shape Rg shape_rg	49.49 Å
Total Rg total_rg	49.76 Å
Total atoms total_atoms	20232
Residues n_residues	2660
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

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

Maximum dimension Dmax dmax	156.5 Å
Rg (real space) rg_real	49.95 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.0000e+09
I(0) uncertainty (real space) i0_real_error	1.6210e+07
Rg (reciprocal space) rg_reciprocal	50.43 Å
I(0) (reciprocal space) i0_reciprocal	1001000000.0000
Solution quality estimate total_estimate	0.8633
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	70.7 Å
Skewness Skewness skewness	-0.055
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	90000000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.847

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Urea-proton symporter DUR3
Molecular weight formula_weight	80662.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20232

MATCPPFDFSTKYYDGDGGCQRQSSFFGGTTVLDQGVGYAVILGFGAFFAVFTSFLVWLEKRYVGARHTSEWFNTAGRNVKTGLIASVIVSQWTWAATILQSSNVAWQYGVSGPFWYASGATIQVLLFGVMAIEIKRKAPNAHTVCEIVKARWGTATHIVFLVFCLATNVVVTAMLLLGGSAVVNALTGVNLYAASFLIPLGVVVYTLAGGLKATFLASYVHSVIVHVALVVFVFLVYTSSKELGSPSVVYDRLKDMVAKSRSCTEPLSHHGQACGPVDGNFRGSYLTMLSSGGAVFGLINIVGNFGTVFVDNGYWVSAIAARPSSTHKGYLLGGLVWFAVPFSLATSLGLGALALDLPISKDEADRGLVPPATAIALMGKSGSLLLLTMLFMAVTSAGSSELIAVSSLFTYDIYRTYINPRATGRQILKISRCAVLGFGCFMGILAVVLNKAGVSLGWMYLAMGVLIGSAVIPIAFMLLWSKANAFGAILGATSGCVFGIITWLTTAKTQYGRVDLDSTGKNGPMLAGNLVAILTGGLIHAVCSLVRPQNYDWSTTREIKVVEAYASGDEDVDVPAEELREEKLRRAKAWIVKWGLVFTILIVVIWPVLSLPARVFSRGYFWFWAIVAIAWGTIGSIVIIGLPLVESWDTIKSVCMGMFTNDRVMKKLDDLNHRLRALTMAVPEAEKIYLLELEKTKKNDEEGVDELTSRGRDYKDDDDKWSHPQFEKGGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	UREA
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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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	3.190 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.19 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	174450

fit	/app/data/saxs_computation/x5/9x5u/9x5u.fit
pddf	/app/data/pr_computation/x5/9x5u/9x5u.pr.out
profile	/app/data/saxs_computation/x5/9x5u/9x5u.dat

Arabidopsis thaliana URE transporter DUR3 - URE bound

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

Urea-proton symporter DUR3

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)