9ymg

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

Method: X-RAY DIFFRACTION

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

Tubulin alpha-1B chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Tubulin beta chain × 1 （P02554） Kinesin-like protein KIF18A, DARPin fusion protein × 1 （Q8NI77） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 1,2-ETHANEDIOL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Tubulin beta chain × 1 （P02554） Kinesin-like protein KIF18A, DARPin fusion protein × 1 （Q8NI77） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	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 1–451； UniProt 1–451 Author chain D； PDBConstruct 1–451； UniProt 1–451

Tubulin beta chain

OrganismNot specified

UniProt P02554

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Tubulin alpha-1B chain × 1 （Q2XVP4） Kinesin-like protein KIF18A, DARPin fusion protein × 1 （Q8NI77） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 1,2-ETHANEDIOL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Tubulin alpha-1B chain × 1 （Q2XVP4） Kinesin-like protein KIF18A, DARPin fusion protein × 1 （Q8NI77） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBB_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–444； UniProt 1–444 Author chain E； PDBConstruct 1–444； UniProt 1–444

Kinesin-like protein KIF18A, DARPin fusion protein

synthetic construct

UniProt Q8NI77

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Tubulin alpha-1B chain × 1 （Q2XVP4） Tubulin beta chain × 1 （P02554） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 1,2-ETHANEDIOL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Tubulin alpha-1B chain × 1 （Q2XVP4） Tubulin beta chain × 1 （P02554） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 3 GUANOSINE-5'-DIPHOSPHATE × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KI18A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–370； UniProt 1–367 Author chain F； PDBConstruct 4–370； UniProt 1–367

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	9ymg
Deposition date deposition_date	2025-10-09
Structure title title	Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin
Keywords keywords	kinesin, motor protein, microtubule, complex; MOTOR 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.

9ymg__assembly_1__model_1

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

Download this curve (.dat)

9ymg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ymg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.77 Å
Rg (electron density)	35.44 Å
Total Rg	35.88 Å
Atom count	10573
Residues	1347
Excluded volume	186980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ymg__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ymg__assembly_2__model_1`	trimeric （3）	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 (9)

Entity 1 Entity 1 polymer

Description description	Tubulin alpha-1B chain
Molecular weight formula_weight	50204.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	21620

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 Entity 2 polymer

Description description	Tubulin beta chain
Molecular weight formula_weight	49793.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEEEDFGEEAEEEA

Entity 3 Entity 3 polymer

Description description	Kinesin-like protein KIF18A, DARPin fusion protein
Molecular weight formula_weight	59769.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNAMSVTEEDLCHHMKVVVRVRPENTKEKAAGFHKVVHVVDKHILVFDPKQEEVSFFHGKKTTNQNVIKKQNKDLKFVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTMLGSADEPGVMYLTMLHLYKCMDEIKEEKICSTAVSYLEVYNEQIRDLLVNSGPLAVREDTQKGVVVHGLTLHQPKSSEEILHLLDNGNKNRTQHPTDMNATSSRSHAVFQIYLRQQDKTASINQNVRIAKMSLIDLAGSERASTSGAKGTRFVEGTNINRSLLALGNVINALADSKRKNQHIPYRNSKLTRLLKDSLGGNCQTIMIAAVSPSSVFYDDTYNTLKYANRAKDIKSSLKSNVLNVNGGGGSGGGGSGGGGSGGGGSGGGGSGGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 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 8 Entity 8 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	455

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Unit-cell length a length_a	105.380 Å
Unit-cell length b length_b	135.470 Å
Unit-cell length c length_c	117.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.406 Å
Low-resolution limit resolution_low	48.673 Å
R factor r_factor	—
R_work r_work	0.1907
R_free r_free	0.2377

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

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

Tubulin alpha-1B chain

State in the Current Structure

Other States of the Same Protein in the Database

Tubulin beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Kinesin-like protein KIF18A, DARPin fusion protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9ymg__assembly_1__model_1

9ymg__assembly_1__model_1 | I(q)

9ymg__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

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 water

7. Citations (1)

Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin

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

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 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

Kinesin-like protein KIF18A, DARPin fusion protein

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

9ymg__assembly_1__model_1

9ymg__assembly_1__model_1 | I(q)

9ymg__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

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 water

7. Citations (1)