SAXSdb — 8rgi

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

Dynein light chain Tctex-type 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 A； UniProt 2–113	Not recorded	Dynein light chain Tctex-type protein 2B × 1 （Q8WW35）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；DYNLT1-DYNLT2B was crystallized using the hanging-drop vapour diffusion method by mixing 1 ul of protein solution (15 mg/ml) with 1-2 ul of precipitant (1.2-1.4 M potassium sodium tartrate, Tris pH 8-8.5) and incubating at 20 degrees Celsius. Crystals were cryo-protected in mother liquor supplemented with 25-30% glycerol and then flash frozen in liquid nitrogen.	Resolution 2.02 Å R-free 0.259

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 8RGI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JPW Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB Deposited 2016-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–113（113 aa） Fragment：UNP residues 1-113,UNP residues 134-154 Chain B 1–113（113 aa） Fragment：UNP residues 1-113,UNP residues 134-154	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure 1 NMR sample composition 100 uM DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 100 uM [U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 100 uM [U-99% 13C; U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8J07 96nm repeat of human respiratory doublet microtubule and associated axonemal complexes Deposited 2023-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 974 PDB declaration: 974-meric	Chain l8 1–113（113 aa） Chain n8 1–113（113 aa） Chain p8 1–113（113 aa） Chain r8 1–113（113 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 285 MG MAGNESIUM ION × 285 GDP GUANOSINE-5'-DIPHOSPHATE × 289	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8PR0 Cytoplasmic dynein-A heavy chain bound to dynactin-p150glued and IC-LC tower Deposited 2023-07-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain G 1–113（113 aa） Chain H 1–113（113 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.40 Å
8PR1 Cytoplasmic dynein-B heavy chain bound to IC-LC tower Deposited 2023-07-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
8PTK Composite structure of Dynein-Dynactin-JIP3-LIS1 Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 53 PDB declaration: 53-meric	Chain k 1–113（113 aa） Chain l 1–113（113 aa） Chain v 1–113（113 aa） Chain y 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 16 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ZN ZINC ION × 3 MG MAGNESIUM ION × 6 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.00 Å
9BLY Composite structure of full-length human dynein-1 in phi-particle conformation Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 5 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9E12 Full-length human dynein-1 in phi comformation under Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9E13 Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9E14 Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.00 Å
9E23 Cryo-EM structure of Pre-Chi dynein tail Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain k 1–113（113 aa） Chain v 1–113（113 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.20 Å
9E28 Cryo-EM structure of Phi dynein tail Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain k 1–113（113 aa） Chain v 1–113（113 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.40 Å
9YNE Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain k 1–113（113 aa） Chain v 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.46 Å
9YNH Full-length human cytoplasmic dynein-1 in phi-like state bound to dynactin-p150glued and LIS1 Deposited 2025-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain K 1–113（113 aa） Chain L 1–113（113 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.50 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYLT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–113； UniProt 2–113

Dynein light chain Tctex-type protein 2B

Homo sapiens

UniProt Q8WW35

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 2–142	Not recorded	Dynein light chain Tctex-type 1 × 1 （P63172）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；DYNLT1-DYNLT2B was crystallized using the hanging-drop vapour diffusion method by mixing 1 ul of protein solution (15 mg/ml) with 1-2 ul of precipitant (1.2-1.4 M potassium sodium tartrate, Tris pH 8-8.5) and incubating at 20 degrees Celsius. Crystals were cryo-protected in mother liquor supplemented with 25-30% glycerol and then flash frozen in liquid nitrogen.	Resolution 2.02 Å R-free 0.259

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 8RGI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8J07 96nm repeat of human respiratory doublet microtubule and associated axonemal complexes Deposited 2023-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 974 PDB declaration: 974-meric	Chain l7 1–142（142 aa） Chain n7 1–142（142 aa） Chain p7 1–142（142 aa） Chain r7 1–142（142 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 285 MG MAGNESIUM ION × 285 GDP GUANOSINE-5'-DIPHOSPHATE × 289	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYT2B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–142； UniProt 2–142

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	8rgi
Deposition date deposition_date	2023-12-13
Structure title title	Structure of DYNLT1:DYNLT2B (TCTEX1:TCTEX1D2) heterodimer.
Keywords keywords	dynein, cilia, intraflagellar transport, complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.80 Å
Radius of gyration Rg (electron density) rg_electron	17.63 Å
Forward intensity I(0) i0	12203600.00
Molecular weight molecular_weight	26076.0 kDa
Excluded volume excluded_volume	32601 Å³
Envelope volume envelope_volume	37382 Å³
Hydration-shell volume shell_volume	17642 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	23.97 Å
Envelope Rg envelope_rg	18.05 Å
Shape Rg shape_rg	17.65 Å
Total Rg total_rg	18.56 Å
Total atoms total_atoms	1830
Residues n_residues	234
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	65.1 Å
Rg (real space) rg_real	18.71 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.2200e+07
I(0) uncertainty (real space) i0_real_error	1.6180e+05
Rg (reciprocal space) rg_reciprocal	18.72 Å
I(0) (reciprocal space) i0_reciprocal	12200000.0000
Solution quality estimate total_estimate	0.8621
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.213
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5634000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.982

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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	Dynein light chain Tctex-type 1
Molecular weight formula_weight	12417.9 kDa
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	1830

SEDYQAAEETAFVVDEVSNIVKEAIESAIGGNAYQHSKVNQWTTNVVEQTLSQLTKLGKPFKYIVTCVIMQKNGAGLHTASSCFWDSSTDGSCTVRWENKTMYCIVSAFGLSI

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 2 Entity 2 polymer

Description description	Dynein light chain Tctex-type protein 2B
Molecular weight formula_weight	16095.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SATSIGVSFSVGDGVPEAEKNAGEPENTYILRPVFQQRFRPSVVKDCIHAVLKEELANAEYSPEEMPQLTKHLSENIKDKLKEMGFDRYKMVVQVVIGEQRGEGVFMASRCFWDADTDNYTHDVFMNDSLFCVVAAFGCFYY

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

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8. Citations (1)

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Unit-cell length a length_a	78.149 Å
Unit-cell length b length_b	78.149 Å
Unit-cell length c length_c	112.560 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.020 Å
Low-resolution limit resolution_low	45.680 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	0.2586

fit	/app/data/saxs_computation/rg/8rgi/8rgi.fit
pddf	/app/data/pr_computation/rg/8rgi/8rgi.pr.out
profile	/app/data/saxs_computation/rg/8rgi/8rgi.dat

Structure of DYNLT1:DYNLT2B (TCTEX1:TCTEX1D2) heterodimer.

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

Dynein light chain Tctex-type 1

State in the Current Structure

Other States of the Same Protein in the Database

Dynein light chain Tctex-type protein 2B

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)