3vkh

X-ray structure of a functional full-length dynein motor domain

Method: X-RAY DIFFRACTION

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

Dynein heavy chain, cytoplasmic

Dictyostelium discoideum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 4	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DYHC_DICDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–3367； UniProt 1388–4730 Author chain B； PDBConstruct 25–3367； UniProt 1388–4730

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	3vkh
Deposition date deposition_date	2011-11-16
Structure title title	X-ray structure of a functional full-length dynein motor domain
Keywords keywords	AAA+ protein, molecular motor, microtubles, motor protein; 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.

3vkh__assembly_1__model_1

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

Download this curve (.dat)

3vkh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vkh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.14 Å
Rg (electron density)	64.28 Å
Total Rg	64.28 Å
Atom count	23482
Residues	3042
Excluded volume	418300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vkh__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vkh__assembly_2__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Dynein heavy chain, cytoplasmic
Molecular weight formula_weight	384331.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	45974

MTRHHHHHHGGGDYKDDDDKGGGKVPVEEEIQDLKAVWVELSNTWQEIDSLKETAWSAIIPRKVRKSLEDTLQKLKNLPNRIRQYSAFDHAQNLIKIYLKGNAIITDLHSEAIKDRHWKILKKRLNTNWIITELTLGSIWDSDLARNENIYREVITAAQGEIALEEFLKGVREFWTTLELDLVNYQRKCKLVRGWDDLFNKLAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLERQRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEGETVTFKKPISIANGPKIHEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWVDNYPTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQEQLQSIEQTTQMILNNLADSVLQDLSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLVIHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAMIKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAGGIKRKCQPPQLPPITDAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKAITKDQLFGSLDLTTREWTDGLFTATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVRVMFEVQDLKYATLATISRCGMVWFSEEILTTQMIFQNYLDTLSNEPFDPQEKEQQKRNENAQLQQQQQTTITSPILTSPPTTSSSSRSTTSTTSMIPAGLKVQKECAAIISQYFEPGGLVHKVLEDAGQRPHIMDFTRLRVLNSFFSLMNRSIVNVIEYNQLHSDFPMSPENQSNYITNRLLYSLMWGLGGSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDDANWSLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKIDEVALKHFPSVNLDALKRPILYSNWLTKDYQPVNRSDLREYVKARLKVFYEEELDVPLVLFNEVLDHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGEEFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNPASPDFHNRSATSPALFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPPVFIQEAEIMGNNLMAIPPSHRDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTPRHYLDFINQVVLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLAQKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPAIIEAQEAVSTIKKKHLDEIKSLPKPPTPVKLAMEAVCLMLGGKKLEWADIRKKIMEPNFITSIINYDTKKMMTPKIREAITKGYLEDPGFDYETVNRASKACGPLVKWATAQTYYSEILDRIKPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPSFLSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSFLDSSFMKNLESALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGDQDVDFSPSFMIFLFTRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEFQVKLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFNRVTRTLLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKETIPQLDSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWIVAQAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMANIVEKEVKSSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYAAAKSGTWVLLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPGVKANLLHTFIGIPATRMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADLRGALDSIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQLFTPSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKARKMINDLQKMQSSEEDGEDDQVSGSSKKESSSSSSEDKGKAKLRATITEWTKLLPKPLKQLKRTTQNIKDPLFRCFEREISTGGKLVKKITNDLANLLELISGNIKSTNYLRSLTTSISKGIVPKEWKWYSVPETISLSVWISDFSKRMQQLSEISESSDYSSIQVWLGGLLNPEAYITATRQSASQLNGWSLENLRLHASSLGKISSEGGASFNVKGMALEGAVWNNDQLTPTDILSTPISIATLTWKDKDDPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISSWKSDI

Source Source

Source organism organism	Dictyostelium discoideum
Common name common_name	Slime mold
NCBI taxonomy ID ncbi_taxonomy_id	44689
Host organism host_organism	Dictyostelium discoideum

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 37 domains

CATH v4.4 (37 domains)

Domain ID domain_id	3vkhA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

Domain ID domain_id	3vkhA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	180 — Split barrel-like
Homologous superfamily homologous superfamily	20 — Dynein motor heavy chain, linker domain, subdomain 3

Domain ID domain_id	3vkhA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1120 — Dynein motor heavy chain, linker domain, subdomain 4

Domain ID domain_id	3vkhA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	710 — Dynein motor, AAA1 domain, small subdomain

Domain ID domain_id	3vkhA06
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhA07
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	130 — Dynein motor, AAA2 domain, small subdomain

Domain ID domain_id	3vkhA08
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhA09
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3vkhA10
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3vkhA11
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3vkhA12
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhA13
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 —

Domain ID domain_id	3vkhA14
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1220 —

Domain ID domain_id	3vkhA16
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhA17
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	720 — Region D6 of dynein motor

Domain ID domain_id	3vkhA18
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	280 —

Domain ID domain_id	3vkhA19
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	490 — Hypothetical upf0131 protein ytfp
Homologous superfamily homologous superfamily	20 — Dynein motor C sequence, barrel region

Domain ID domain_id	3vkhB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2620 —

Domain ID domain_id	3vkhB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	100 — Dynein motor heavy chain, linker domain, N-terminal subdomain

Domain ID domain_id	3vkhB03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	180 — Split barrel-like
Homologous superfamily homologous superfamily	20 — Dynein motor heavy chain, linker domain, subdomain 3

Domain ID domain_id	3vkhB04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1120 — Dynein motor heavy chain, linker domain, subdomain 4

Domain ID domain_id	3vkhB05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	710 — Dynein motor, AAA1 domain, small subdomain

Domain ID domain_id	3vkhB07
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB08
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	130 — Dynein motor, AAA2 domain, small subdomain

Domain ID domain_id	3vkhB09
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB10
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3vkhB11
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB12
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3vkhB13
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2610 —

Domain ID domain_id	3vkhB14
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB15
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 —

Domain ID domain_id	3vkhB17
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vkhB18
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	720 — Region D6 of dynein motor

Domain ID domain_id	3vkhB19
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	280 —

Domain ID domain_id	3vkhB20
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	490 — Hypothetical upf0131 protein ytfp
Homologous superfamily homologous superfamily	20 — Dynein motor C sequence, barrel region

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Unit-cell length a length_a	195.726 Å
Unit-cell length b length_b	228.955 Å
Unit-cell length c length_c	201.168 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	3.800 Å
Low-resolution limit resolution_low	48.790 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2920

X-ray structure of a functional full-length dynein motor domain

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

Dynein heavy chain, cytoplasmic

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

3vkh__assembly_1__model_1

3vkh__assembly_1__model_1 | I(q)

3vkh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 37 domains

CATH v4.4 (37 domains)

7. Citations (2)

X-ray structure of a functional full-length dynein motor domain

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

Dynein heavy chain, cytoplasmic

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

3vkh__assembly_1__model_1

3vkh__assembly_1__model_1 | I(q)

3vkh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 37 domains

CATH v4.4 (37 domains)

7. Citations (2)