SAXSdb — 4icv

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

Tubulin-specific chaperone E

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 443–527	Fragment：Ubiquitin-like domain, UNP residues 443-527	PR PRASEODYMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM Bis Tris pH 6.5 and 43 % (v/v) PEG 400 and 10 mM praseodymium (III) acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.45 Å R-free 0.189

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 4ICV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ICU Ubiquitin-like domain of human tubulin folding cofactor E - crystal from A Deposited 2012-12-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 443–527（85 aa） Fragment：Ubiquitin-like domain, UNP residues 443-527	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris pH 8.5, 200 mM sodium acetate and 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.263
4ICU Ubiquitin-like domain of human tubulin folding cofactor E - crystal from A Deposited 2012-12-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 443–527（85 aa） Fragment：Ubiquitin-like domain, UNP residues 443-527	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris pH 8.5, 200 mM sodium acetate and 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.263
4ICU Ubiquitin-like domain of human tubulin folding cofactor E - crystal from A Deposited 2012-12-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 443–527（85 aa） Fragment：Ubiquitin-like domain, UNP residues 443-527	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris pH 8.5, 200 mM sodium acetate and 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.263
4ICU Ubiquitin-like domain of human tubulin folding cofactor E - crystal from A Deposited 2012-12-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 443–527（85 aa） Fragment：Ubiquitin-like domain, UNP residues 443-527	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris pH 8.5, 200 mM sodium acetate and 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.263
9M1J Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex 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 × 4 PDB declaration: tetrameric	Chain E 129–527（399 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.14 Å
9M1K Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex with GTP 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 × 4 PDB declaration: tetrameric	Chain E 1–527（527 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.45 Å
9M1L Cryo-EM structure of the TBC-DE-Arl2-alpha-beta-tubulin complex with GTP 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 E 1–527（527 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
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 E 1–527（527 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

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TBCE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 443–527

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	4icv
Deposition date deposition_date	2012-12-11
Structure title title	Ubiquitin-like domain of human tubulin folding cofactor E - crystal form B
Keywords keywords	Ubiquitin-like domain, tubulin folding cofactor, alpha tubulin, tubulin folding cofactor B, CHAPERONE; CHAPERONE
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	13.89 Å
Radius of gyration Rg (electron density) rg_electron	12.35 Å
Forward intensity I(0) i0	2175890.00
Molecular weight molecular_weight	10117.0 kDa
Excluded volume excluded_volume	12656 Å³
Envelope volume envelope_volume	14362 Å³
Hydration-shell volume shell_volume	10085 Å³
Envelope diameter envelope_diameter	41.3 Å
Shell Rg shell_rg	17.81 Å
Envelope Rg envelope_rg	12.53 Å
Shape Rg shape_rg	12.22 Å
Total Rg total_rg	14.04 Å
Total atoms total_atoms	685
Residues n_residues	84
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	42.0 Å
Rg (real space) rg_real	13.77 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.1760e+06
I(0) uncertainty (real space) i0_real_error	2.3090e+04
Rg (reciprocal space) rg_reciprocal	13.78 Å
I(0) (reciprocal space) i0_reciprocal	2176000.0000
Solution quality estimate total_estimate	0.8121
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.2 Å
Skewness Skewness skewness	-0.007
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	306500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tubulin-specific chaperone E
Molecular weight formula_weight	9819.5 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	892

NQLLTLKIKYPHQLDQKVLEKQLPGSMTIQKVKGLLSRLLKVPVSDLLLSYESPKKPGREIELENDLKSLQFYSVENGDCLLVRW

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 non-polymer

Description description	PRASEODYMIUM ION
Molecular weight formula_weight	140.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4icva_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

CATH v4.4 (1 domains)

Domain ID domain_id	4icvA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	42.270 Å
Unit-cell length b length_b	65.830 Å
Unit-cell length c length_c	73.570 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1632
R_work r_work	0.1619
R_free r_free	0.1888

fit	/app/data/saxs_computation/ic/4icv/4icv.fit
pddf	/app/data/pr_computation/ic/4icv/4icv.pr.out
profile	/app/data/saxs_computation/ic/4icv/4icv.dat

Ubiquitin-like domain of human tubulin folding cofactor E - crystal form B

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

Tubulin-specific chaperone E

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