SAXSdb — 2l3l

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

Tubulin-specific chaperone C

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–135	Fragment：UNP RESIDUES 26-135	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition：0.5-1.0 mM [U-13C; U-15N] TBCC_Nterm-1, 20 mM potassium phosphate-2, 20 mM potassium chloride-3, 1.0 mM TCEP-4, 1.0 mM EDTA-5, 0.05 mM DSS-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2L3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YUH Solution structure of the C-terminal region in human tubulin folding cofactor C Deposited 2007-04-06	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 181–346（166 aa） Fragment：C-terminal region	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1mM protein, 20mM d-Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
9M1M Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–346（346 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.21 Å
9M1N Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–346（346 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.24 Å

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

View Construct and Data Evidence

UniProt name	TBCC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–111； UniProt 26–135

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	2l3l
Deposition date deposition_date	2010-09-14
Structure title title	The solution structure of the N-terminal domain of human Tubulin Binding Cofactor C reveals a platform for the interaction with ab-tubulin
Keywords keywords	CHAPERONE, tubulin binding cofactor; CHAPERONE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	21.84 Å
Radius of gyration Rg (electron density) rg_electron	21.37 Å
Forward intensity I(0) i0	1092790000.00
Molecular weight molecular_weight	262980.0 kDa
Excluded volume excluded_volume	324530 Å³
Envelope volume envelope_volume	100920 Å³
Hydration-shell volume shell_volume	29830 Å³
Envelope diameter envelope_diameter	100.1 Å
Shell Rg shell_rg	35.38 Å
Envelope Rg envelope_rg	28.93 Å
Shape Rg shape_rg	21.27 Å
Total Rg total_rg	22.07 Å
Total atoms total_atoms	37340
Residues n_residues	2220
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	86.5 Å
Rg (real space) rg_real	22.12 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	1.0930e+09
I(0) uncertainty (real space) i0_real_error	1.5390e+07
Rg (reciprocal space) rg_reciprocal	22.07 Å
I(0) (reciprocal space) i0_reciprocal	1093000000.0000
Solution quality estimate total_estimate	0.5292
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.8 Å
Skewness Skewness skewness	0.510
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1400000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.409; Stabil: 0.999; Sysdev: 0.207; Positv: 1.000; Valcen: 0.116; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2l3lA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1250 — Tubulin Binding Cofactor C, N-terminal domain

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8. Citations (2)

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Description description	Tubulin-specific chaperone C
Molecular weight formula_weight	13169.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	37340

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

fit	/app/data/saxs_computation/l3/2l3l/2l3l.fit
pddf	/app/data/pr_computation/l3/2l3l/2l3l.pr.out
profile	/app/data/saxs_computation/l3/2l3l/2l3l.dat

The solution structure of the N-terminal domain of human Tubulin Binding Cofactor C reveals a platform for the interaction with ab-tubulin

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

Tubulin-specific chaperone C

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)