3dco

Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule

Method: ELECTRON MICROSCOPY

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

Kinesin-like protein Nod

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Bovine Alpha Tubulin × 1 Bovine Beta Tubulin × 1 MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 ZINC ION × 1 GUANOSINE-5'-TRIPHOSPHATE × 1 GUANOSINE-5'-DIPHOSPHATE × 1 TAXOL × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOD_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain N； PDBConstruct 16–333； UniProt 1–318

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	3dco
Deposition date deposition_date	2008-06-04
Structure title title	Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule
Keywords keywords	;kinesin, catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, cryo-EM, 3D reconstruction, tubulin, nucleotide-free, ATP-binding, Coiled coil, Motor protein, Nucleotide-binding ;; MOTOR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

3dco__assembly_1__model_1

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

Download this curve (.dat)

3dco__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dco__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.35 Å
Rg (electron density)	31.62 Å
Total Rg	32.21 Å
Atom count	8977
Residues	1129
Excluded volume	158770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dco__assembly_1__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	Kinesin-like protein Nod
Molecular weight formula_weight	38305.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N
Atom count atom_count	8977

MASDYKDDDDKRRRGMEGAKLSAVRIAVREAPYRQFLGRREPSVVQFPPWSDGKSLIVDQNEFHFDHAFPATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSMGMTPPGEILPEHLGILPRALGDIFERVTARQENNKDAIQVYASFIEIYNEKPFDLLGSTPHMPMVAARCQRCTCLPLHSQADLHHILELGTRNRRVRPTNMNSNSSRSHAIVTIHVKSKTHHSRMNIVDLAGSEGVRRTGHEGVARQEGVNINLGLLSINKVVMSMAAGHTVIPYRDSVLTTVLQASLTAQSYLTFLACISPHQCDLSETLSTLRFGTSAKAAALEHHHHHH

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Bovine Alpha Tubulin
Molecular weight formula_weight	50107.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 3 Entity 3 polymer

Description description	Bovine Beta Tubulin
Molecular weight formula_weight	49907.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 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 8 Entity 8 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 9 Entity 9 non-polymer

Description description	TAXOL
Molecular weight formula_weight	853.9 kDa
Source method src_method	syn
Copy count entity_count	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	1

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

Resolution resolution	11.000 Å
Low-resolution limit resolution_low	19.050 Å
R factor r_factor	—
R_work r_work	0.2270
R_free r_free	0.2550

Resolution resolution	11.00 Å
Resolution测定Method resolution_method	Helical 3D reconstruction
颗粒数 num_particles	—

Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule

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

Kinesin-like protein Nod

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

3dco__assembly_1__model_1

3dco__assembly_1__model_1 | I(q)

3dco__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 non-polymer

7. Citations (1)

Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule

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

Kinesin-like protein Nod

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

3dco__assembly_1__model_1

3dco__assembly_1__model_1 | I(q)

3dco__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 non-polymer

7. Citations (1)