5itz

Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin

Method: X-RAY DIFFRACTION

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt P81947

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tubulin beta-2B chain × 1 （Q6B856） Centromere protein J × 1 （Q9HC77） Designed ankyrin repeat protein (DARPIN) D1 × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBA1B_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–451； UniProt 1–451

Tubulin beta-2B chain

OrganismNot specified

UniProt Q6B856

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tubulin alpha-1B chain × 1 （P81947） Centromere protein J × 1 （Q9HC77） Designed ankyrin repeat protein (DARPIN) D1 × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 water × 4	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 1–445； UniProt 1–445

Centromere protein J

Homo sapiens

UniProt Q9HC77

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tubulin alpha-1B chain × 1 （P81947） Tubulin beta-2B chain × 1 （Q6B856） Designed ankyrin repeat protein (DARPIN) D1 × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CENPJ_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 18–129； UniProt 311–422

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	5itz
Deposition date deposition_date	2016-03-17
Structure title title	Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin
Keywords keywords	Tubulin, CPAP, Centriole, 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.

5itz__assembly_1__model_1

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

Download this curve (.dat)

5itz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5itz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.74 Å
Rg (electron density)	33.79 Å
Total Rg	34.13 Å
Atom count	7792
Residues	990
Excluded volume	137920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5itz__assembly_1__model_1`	tetrameric （4）	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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8279

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 Entity 2 polymer

Description description	Tubulin beta-2B chain
Molecular weight formula_weight	49999.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

Entity 3 Entity 3 polymer

Description description	Centromere protein J
Molecular weight formula_weight	14889.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAHHHHHHGSLVPRGSAQKHDDSSEVANIEERPIKAAIGERKQTFEDYLEEQIQLEEQELKQKQLKEAEGPLPIKAKPKQPFLKRGEGLARFTNAKSKFQKGKESKLVTNQSTSEDQPLFKMDRQQLQR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Designed ankyrin repeat protein (DARPIN) D1
Molecular weight formula_weight	13355.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

DLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADV

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	1

Entity 8 Entity 8 non-polymer

Description description	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
Molecular weight formula_weight	399.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	473

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	5itzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	5itzA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	5itzA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	5itzB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	5itzB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	5itzB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	5itzF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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Unit-cell length a length_a	61.080 Å
Unit-cell length b length_b	85.340 Å
Unit-cell length c length_c	98.690 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	52.644 Å
R factor r_factor	0.1789
R_work r_work	0.1773
R_free r_free	0.2174

Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin

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-2B chain

State in the Current Structure

Other States of the Same Protein in the Database

Centromere protein J

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

5itz__assembly_1__model_1

5itz__assembly_1__model_1 | I(q)

5itz__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 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 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin

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-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

Centromere protein J

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

5itz__assembly_1__model_1

5itz__assembly_1__model_1 | I(q)

5itz__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 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 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)