6mdm

The 20S supercomplex engaging the SNAP-25 N-terminus (class 1)

Method: ELECTRON MICROSCOPY

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

Vesicle-fusing ATPase

Cricetulus griseus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Synaptosomal-associated protein 25 × 1 （P60881） Syntaxin-1A × 1 （P32851） Vesicle-associated membrane protein 2 × 1 （P63045） Alpha-soluble NSF attachment protein × 2 （P54921） ADENOSINE-5'-TRIPHOSPHATE × 9 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NSF_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–768； UniProt 1–744 Author chain B； PDBConstruct 25–768； UniProt 1–744 Author chain C； PDBConstruct 25–768； UniProt 1–744 Author chain D； PDBConstruct 25–768； UniProt 1–744 Author chain E； PDBConstruct 25–768； UniProt 1–744 Author chain F； PDBConstruct 25–768； UniProt 1–744

Synaptosomal-associated protein 25

Rattus norvegicus

UniProt P60881

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Vesicle-fusing ATPase × 6 （P18708） Syntaxin-1A × 1 （P32851） Vesicle-associated membrane protein 2 × 1 （P63045） Alpha-soluble NSF attachment protein × 2 （P54921） ADENOSINE-5'-TRIPHOSPHATE × 9 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNP25_RAT
Isoform	P60881-2
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 4–207； UniProt 1–204

Syntaxin-1A

Rattus norvegicus

UniProt P32851

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Vesicle-fusing ATPase × 6 （P18708） Synaptosomal-associated protein 25 × 1 （P60881） Vesicle-associated membrane protein 2 × 1 （P63045） Alpha-soluble NSF attachment protein × 2 （P54921） ADENOSINE-5'-TRIPHOSPHATE × 9 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STX1A_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–256； UniProt 1–256

Vesicle-associated membrane protein 2

Rattus norvegicus

UniProt P63045

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Vesicle-fusing ATPase × 6 （P18708） Synaptosomal-associated protein 25 × 1 （P60881） Syntaxin-1A × 1 （P32851） Alpha-soluble NSF attachment protein × 2 （P54921） ADENOSINE-5'-TRIPHOSPHATE × 9 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAMP2_RAT
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain J； PDBConstruct 29–117； UniProt 1–89

Alpha-soluble NSF attachment protein

Rattus norvegicus

UniProt P54921

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Vesicle-fusing ATPase × 6 （P18708） Synaptosomal-associated protein 25 × 1 （P60881） Syntaxin-1A × 1 （P32851） Vesicle-associated membrane protein 2 × 1 （P63045） ADENOSINE-5'-TRIPHOSPHATE × 9 ADENOSINE-5'-DIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNAA_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 19–313； UniProt 1–295 Author chain L； PDBConstruct 19–313； UniProt 1–295

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	6mdm
Deposition date deposition_date	2018-09-04
Structure title title	The 20S supercomplex engaging the SNAP-25 N-terminus (class 1)
Keywords keywords	SNARE, NSF, SNAP, ATPase, AAA, disassembly, synapse, membrane fusion, exocytosis, HYDROLASE; HYDROLASE
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.

6mdm__assembly_1__model_1

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

Download this curve (.dat)

6mdm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mdm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	61.69 Å
Rg (electron density)	61.70 Å
Total Rg	61.72 Å
Atom count	73303
Residues	4651
Excluded volume	652730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mdm__assembly_1__model_1`	undecameric （11）	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 (7)

Entity 1 Entity 1 polymer

Description description	Vesicle-fusing ATPase
Molecular weight formula_weight	85509.2 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	73303

MGHHHHHHDYDIPTTENLYFQGAHMAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVRTSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKAKTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFASRVFPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNAREPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDEKGRLQILHIHTARMRGHQLLSADVDIKELAVETKNFSGAELEGLVRAAQSTAMNRHIIASTKVEVDMEKAESLQVTRGDFLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLDFD

Source Source

Source organism organism	Cricetulus griseus
Common name common_name	Chinese hamster
NCBI taxonomy ID ncbi_taxonomy_id	10029
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Synaptosomal-associated protein 25
Molecular weight formula_weight	23512.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MASMAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGKCCGLFICPCNKLKSSDAYKKAWGNNQDGVVASQPARVVDEREQMAISGGFIRRVTNDARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG

Source Source

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

Entity 3 Entity 3 polymer

Description description	Syntaxin-1A
Molecular weight formula_weight	29634.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTLSRKFVEVMSEYNATQSDYRERSKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASGIIMDSSISKQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVK

Source Source

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

Entity 4 Entity 4 polymer

Description description	Vesicle-associated membrane protein 2
Molecular weight formula_weight	12981.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MASYYHHHHHHDYDIPTSENLYFQGASHMSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW

Source Source

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

Entity 5 Entity 5 polymer

Description description	Alpha-soluble NSF attachment protein
Molecular weight formula_weight	35598.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,L

MHHHHHHHHHHENLYFQGMDTSGKQAEAMALLAEAERKVKNSQSFFSGLFGGSSKIEEACEIYARAANMFKMAKNWSAAGNAFCQAAQLHLQLQSKHDAATCFVDAGNAFKKADPQEAINCLMRAIEIYTDMGRFTIAAKHHISIAEIYETELVDVEKAIAHYEQSADYYKGEESNSSANKCLLKVAGYAAQLEQYQKAIDIYEQVGTSAMDSPLLKYSAKDYFFKAALCHFCIDMLNAKLAVQKYEELFPAFSDSRECKLMKKLLEAHEEQNVDSYTESVKEYDSISRLDQWLTTMLLRIKKTIQGDEEDLR

Source Source

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

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

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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	triclinic

Resolution resolution	4.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	55150

The 20S supercomplex engaging the SNAP-25 N-terminus (class 1)

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

Vesicle-fusing ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Synaptosomal-associated protein 25

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Syntaxin-1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vesicle-associated membrane protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Alpha-soluble NSF attachment 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

6mdm__assembly_1__model_1

6mdm__assembly_1__model_1 | I(q)

6mdm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)