SAXSdb — 9pnd

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

Tubulin beta-3 chain

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–450 Chain D； UniProt 1–450	Not recorded	Detyrosinated tubulin alpha-1A chain × 2 （P68369） MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 2 EPB 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；Gibco Neurobasal Media 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TBB3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–450； UniProt 1–450 Author chain D； PDBConstruct 1–450； UniProt 1–450

Detyrosinated tubulin alpha-1A chain

OrganismNot specified

UniProt P68369

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–451 Chain C； UniProt 1–451	Not recorded	Tubulin beta-3 chain × 2 （Q9ERD7） MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 2 EPB 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2；Gibco Neurobasal Media 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 9PND	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8IXA GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin non-seam region Deposited 2023-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain A 1–451（451 aa） Chain B 1–451（451 aa） Chain C 1–451（451 aa） Chain D 1–451（451 aa） Chain E 1–451（451 aa） Chain F 1–451（451 aa） Chain G 1–451（451 aa） Chain H 1–451（451 aa） Chain I 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 9 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8IXB GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region Deposited 2023-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–451（451 aa） Chain E 1–451（451 aa） Chain F 1–451（451 aa） Chain H 1–451（451 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 4 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8TO0 48-nm repeating structure of doublets from mouse sperm flagella Deposited 2023-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 471 PDB declaration: 471-meric	Chain A5 1–451（451 aa） Chain A7 1–451（451 aa） Chain A9 1–451（451 aa） Chain AM 1–451（451 aa） Chain AO 1–451（451 aa） Chain AQ 1–451（451 aa） Chain AS 1–451（451 aa） Chain AU 1–451（451 aa） Chain AW 1–451（451 aa） Chain AY 1–451（451 aa） Chain Aj 1–451（451 aa） Chain Al 1–451（451 aa） Chain An 1–451（451 aa） Chain Ap 1–451（451 aa） Chain Ar 1–451（451 aa） Chain At 1–451（451 aa） Chain Av 1–451（451 aa） Chain B0 1–451（451 aa） Chain B2 1–451（451 aa） Chain B4 1–451（451 aa） Chain B8 1–451（451 aa） Chain BA 1–451（451 aa） Chain BC 1–451（451 aa） Chain BE 1–451（451 aa） Chain BO 1–451（451 aa） Chain BQ 1–451（451 aa） Chain BS 1–451（451 aa） Chain BU 1–451（451 aa） Chain BW 1–451（451 aa） Chain BY 1–451（451 aa） Chain Bc 1–451（451 aa） Chain Be 1–451（451 aa） Chain Bg 1–451（451 aa） Chain Bi 1–451（451 aa） Chain Bk 1–451（451 aa） Chain Bm 1–451（451 aa） Chain Br 1–451（451 aa） Chain Bt 1–451（451 aa） Chain Bv 1–451（451 aa） Chain Bx 1–451（451 aa） Chain Bz 1–451（451 aa） Chain C0 1–451（451 aa） Chain C1 1–451（451 aa） Chain C3 1–451（451 aa） Chain C8 1–451（451 aa） Chain CB 1–451（451 aa） Chain CD 1–451（451 aa） Chain CF 1–451（451 aa） Chain CH 1–451（451 aa） Chain CJ 1–451（451 aa） Chain CN 1–451（451 aa） Chain CP 1–451（451 aa） Chain CR 1–451（451 aa） Chain CT 1–451（451 aa） Chain CV 1–451（451 aa） Chain CX 1–451（451 aa） Chain Cc 1–451（451 aa） Chain Ce 1–451（451 aa） Chain Cg 1–451（451 aa） Chain Ci 1–451（451 aa） Chain Ck 1–451（451 aa） Chain Cm 1–451（451 aa） Chain Co 1–451（451 aa） Chain Cs 1–451（451 aa） Chain Cu 1–451（451 aa） Chain Cw 1–451（451 aa） Chain Cy 1–451（451 aa） Chain D2 1–451（451 aa） Chain D5 1–451（451 aa） Chain D7 1–451（451 aa） Chain D9 1–451（451 aa） Chain DB 1–451（451 aa） Chain DD 1–451（451 aa） Chain DF 1–451（451 aa） Chain DH 1–451（451 aa） Chain DM 1–451（451 aa） Chain DO 1–451（451 aa） Chain DQ 1–451（451 aa） Chain DS 1–451（451 aa） Chain DU 1–451（451 aa） Chain DW 1–451（451 aa） Chain Db 1–451（451 aa） Chain Dd 1–451（451 aa） Chain Df 1–451（451 aa） Chain Dh 1–451（451 aa） Chain Dj 1–451（451 aa） Chain Dl 1–451（451 aa） Chain Dp 1–451（451 aa） Chain Dr 1–451（451 aa） Chain Dt 1–451（451 aa） Chain Dv 1–451（451 aa） Chain Dx 1–451（451 aa） Chain Dz 1–451（451 aa） Chain E3 1–451（451 aa） Chain E5 1–451（451 aa） Chain E7 1–451（451 aa） Chain E9 1–451（451 aa） Chain EA 1–451（451 aa） Chain EC 1–451（451 aa） Chain EE 1–451（451 aa） Chain EG 1–451（451 aa） Chain EJ 1–451（451 aa） Chain EL 1–451（451 aa） Chain EN 1–451（451 aa） Chain EP 1–451（451 aa） Chain ER 1–451（451 aa） Chain ET 1–451（451 aa） Chain EV 1–451（451 aa） Chain EY 1–451（451 aa） Chain Ea 1–451（451 aa） Chain Ec 1–451（451 aa） Chain Ee 1–451（451 aa） Chain Eg 1–451（451 aa） Chain Ei 1–451（451 aa） Chain Ek 1–451（451 aa） Chain Eo 1–451（451 aa） Chain Eq 1–451（451 aa） Chain Es 1–451（451 aa） Chain Eu 1–451（451 aa） Chain Ew 1–451（451 aa） Chain Ey 1–451（451 aa） Chain FA 1–451（451 aa） Chain FC 1–451（451 aa） Chain FG 1–451（451 aa） Chain FI 1–451（451 aa） Chain FK 1–451（451 aa） Chain FM 1–451（451 aa） Chain FO 1–451（451 aa） Chain FQ 1–451（451 aa） Chain FU 1–451（451 aa） Chain FW 1–451（451 aa） Chain FY 1–451（451 aa） Chain Fa 1–451（451 aa） Chain Fc 1–451（451 aa） Chain Fe 1–451（451 aa） Chain N 1–451（451 aa） Chain P 1–451（451 aa） Chain R 1–451（451 aa） Chain T 1–451（451 aa） Chain V 1–451（451 aa） Chain X 1–451（451 aa） Chain Z 1–451（451 aa） Chain n 1–451（451 aa） Chain p 1–451（451 aa） Chain r 1–451（451 aa） Chain t 1–451（451 aa） Chain v 1–451（451 aa） Chain x 1–451（451 aa） Chain z 1–451（451 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
9SFP Native cytoplasmic lattices from mouse oocytes Deposited 2025-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain a 1–451（451 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
9XRL Structure of mouse cytoplasmic lattice (CPL) repeating unit Deposited 2025-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 73 PDB declaration: 73-meric	Chain AF 1–451（451 aa） Chain AO 1–451（451 aa） Chain u 1–451（451 aa）	Not recorded	ZN ZINC ION × 13 GTP GUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

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

View Construct and Data Evidence

UniProt name	TBA1A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–451； UniProt 1–451 Author chain C； PDBConstruct 1–451； UniProt 1–451

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	9pnd
Deposition date deposition_date	2025-07-20
Structure title title	In situ microtubule of EpoB-induced regenerating axons
Keywords keywords	cytoskeleton, microtubules, neuroregeneration, axon, STRUCTURAL PROTEIN; STRUCTURAL 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	51.84 Å
Radius of gyration Rg (electron density) rg_electron	52.80 Å
Forward intensity I(0) i0	592869000.00
Molecular weight molecular_weight	196340.0 kDa
Excluded volume excluded_volume	243380 Å³
Envelope volume envelope_volume	330110 Å³
Hydration-shell volume shell_volume	59070 Å³
Envelope diameter envelope_diameter	193.8 Å
Shell Rg shell_rg	46.34 Å
Envelope Rg envelope_rg	53.19 Å
Shape Rg shape_rg	52.80 Å
Total Rg total_rg	52.56 Å
Total atoms total_atoms	13774
Residues n_residues	1734
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	180.7 Å
Rg (real space) rg_real	52.60 Å
Rg uncertainty (real space) rg_real_error	2.47 Å
I(0) (real space) i0_real	5.9290e+08
I(0) uncertainty (real space) i0_real_error	1.4190e+07
Rg (reciprocal space) rg_reciprocal	51.19 Å
I(0) (reciprocal space) i0_reciprocal	591700000.0000
Solution quality estimate total_estimate	0.6820
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.685
Kurtosis Kurtosis kurtosis	-0.319
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	109400000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.386; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.585; Smooth: 0.122

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Tubulin beta-3 chain
Molecular weight formula_weight	50467.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	13778

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEMYEDDDEESEAQGPK

Entity 2 Entity 2 polymer

Description description	Detyrosinated tubulin alpha-1A chain
Molecular weight formula_weight	50188.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

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 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
Molecular weight formula_weight	507.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
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	118551

fit	/app/data/saxs_computation/pn/9pnd/9pnd.fit
pddf	/app/data/pr_computation/pn/9pnd/9pnd.pr.out
profile	/app/data/saxs_computation/pn/9pnd/9pnd.dat

In situ microtubule of EpoB-induced regenerating axons

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

Tubulin beta-3 chain

State in the Current Structure

Other States of the Same Protein in the Database

Detyrosinated tubulin alpha-1A chain

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)