9k7e

Crystal structure of T2R-TTL-taccalonolide Y8 complex

Method: X-RAY DIFFRACTION

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

Detyrosinated tubulin alpha-1B chain

Sus scrofa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tubulin beta-2B chain × 2 （Q6B856） Stathmin-4 × 1 （P63043） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 (4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one × 1 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBA1B_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 1–440 Author chain C； PDBConstruct 1–440； UniProt 1–440

Tubulin beta-2B chain

Bos taurus

UniProt Q6B856

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Stathmin-4 × 1 （P63043） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 (4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one × 1 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBB2B_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431

Stathmin-4

Rattus norvegicus

UniProt P63043

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta-2B chain × 2 （Q6B856） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 (4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one × 1 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STMN4_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–143； UniProt 49–189

Tubulin--tyrosine ligase

Gallus gallus

UniProt A0A8C9FGJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta-2B chain × 2 （Q6B856） Stathmin-4 × 1 （P63043） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 (4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one × 1 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8C9FGJ1_PAVCR
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–378； UniProt 1–378

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	9k7e
Deposition date deposition_date	2024-10-23
Last revision last_revision	2025-11-05
Structure title title	Crystal structure of T2R-TTL-taccalonolide Y8 complex
Keywords keywords	tubulin, inhibitor, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9k7e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9k7e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9k7e__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	55.73 Å
Rg (electron density)	56.64 Å
Total Rg	56.44 Å
Atom count	17389
Residues	2172
Excluded volume	306760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9k7e__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Detyrosinated tubulin alpha-1B chain
Molecular weight formula_weight	48966.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17393

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tubulin beta-2B chain
Molecular weight formula_weight	48391.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD

Source Source

Source organism organism	Bos taurus
Common name common_name	domestic cattle
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Stathmin-4
Molecular weight formula_weight	16844.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKEEASR

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Tubulin--tyrosine ligase
Molecular weight formula_weight	43825.9 kDa
EC 编号 ec_number	6.3.2.25
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQLVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLINNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVHVIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHLTNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEPAISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFPLADTGQKTSQPTSIFIKLHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	(4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 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 10 Entity 10 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 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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Unit-cell length a length_a	104.830 Å
Unit-cell length b length_b	157.190 Å
Unit-cell length c length_c	181.650 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	52.430 Å
R factor r_factor	0.2147
R_work r_work	0.2137
R_free r_free	0.2673

Crystal structure of T2R-TTL-taccalonolide Y8 complex

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

Detyrosinated tubulin alpha-1B chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tubulin beta-2B chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Stathmin-4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tubulin--tyrosine ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9k7e__assembly_1__model_1

9k7e__assembly_1__model_1 | I(q)

9k7e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)