6mti

Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+

Method: ELECTRON MICROSCOPY

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

Synaptotagmin-1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	Vesicle-associated membrane protein 2 × 6 （P63045） Syntaxin-1A × 6 （P32851） Synaptosomal-associated protein 25 × 6 （P60881） Synaptosomal-associated protein 25 × 6 （P60881） MAGNESIUM ION × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYT1_RAT
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain 1； PDBConstruct 1–127； UniProt 141–267 Author chain 6； PDBConstruct 1–127； UniProt 141–267 Author chain 2； PDBConstruct 1–281； UniProt 141–421 Author chain 3； PDBConstruct 1–281； UniProt 141–421 Author chain 4； PDBConstruct 1–281； UniProt 141–421 Author chain 5； PDBConstruct 1–281； UniProt 141–421

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 30	Synaptotagmin-1 × 2 （P21707） Synaptotagmin-1 × 4 （P21707） Syntaxin-1A × 6 （P32851） Synaptosomal-associated protein 25 × 6 （P60881） Synaptosomal-associated protein 25 × 6 （P60881） MAGNESIUM ION × 10	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	3
Chains and sequence ranges	Author chain A； PDBConstruct 2–63； UniProt 28–89 Author chain E； PDBConstruct 2–63； UniProt 28–89 Author chain I； PDBConstruct 2–63； UniProt 28–89 Author chain M； PDBConstruct 2–63； UniProt 28–89 Author chain Q； PDBConstruct 2–63； UniProt 28–89 Author chain U； PDBConstruct 2–63； UniProt 28–89

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 30	Synaptotagmin-1 × 2 （P21707） Synaptotagmin-1 × 4 （P21707） Vesicle-associated membrane protein 2 × 6 （P63045） Synaptosomal-associated protein 25 × 6 （P60881） Synaptosomal-associated protein 25 × 6 （P60881） MAGNESIUM ION × 10	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	4
Chains and sequence ranges	Author chain B； PDBConstruct 2–67； UniProt 191–256 Author chain F； PDBConstruct 2–67； UniProt 191–256 Author chain J； PDBConstruct 2–67； UniProt 191–256 Author chain N； PDBConstruct 2–67； UniProt 191–256 Author chain R； PDBConstruct 2–67； UniProt 191–256 Author chain V； PDBConstruct 2–67； UniProt 191–256

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 30	Synaptotagmin-1 × 2 （P21707） Synaptotagmin-1 × 4 （P21707） Vesicle-associated membrane protein 2 × 6 （P63045） Syntaxin-1A × 6 （P32851） MAGNESIUM ION × 10	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	5, 6
Chains and sequence ranges	Author chain C； PDBConstruct 1–77； UniProt 7–83 Author chain G； PDBConstruct 1–77； UniProt 7–83 Author chain K； PDBConstruct 1–77； UniProt 7–83 Author chain O； PDBConstruct 1–77； UniProt 7–83 Author chain S； PDBConstruct 1–77； UniProt 7–83 Author chain W； PDBConstruct 1–77； UniProt 7–83 Author chain D； PDBConstruct 2–65； UniProt 141–204 Author chain H； PDBConstruct 2–65； UniProt 141–204 Author chain L； PDBConstruct 2–65； UniProt 141–204 Author chain P； PDBConstruct 2–65； UniProt 141–204 Author chain T； PDBConstruct 2–65； UniProt 141–204 Author chain X； PDBConstruct 2–65； UniProt 141–204

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	6mti
Deposition date deposition_date	2018-10-19
Structure title title	Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+
Keywords keywords	SNARE, lipid nanotubes, EXOCYTOSIS; EXOCYTOSIS
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.

6mti__assembly_1__model_1

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

Download this curve (.dat)

6mti__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mti__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	75.69 Å
Rg (electron density)	76.92 Å
Total Rg	76.73 Å
Atom count	23540
Residues	2966
Excluded volume	415450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mti__assembly_1__model_1`	30-meric （30）	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	Synaptotagmin-1
Molecular weight formula_weight	14654.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,6
Atom count atom_count	23540

KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEK

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 2 Entity 2 polymer

Description description	Synaptotagmin-1
Molecular weight formula_weight	32247.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2,3,4,5

KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVKK

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	Vesicle-associated membrane protein 2
Molecular weight formula_weight	7231.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M,Q,U

GSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW

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	Syntaxin-1A
Molecular weight formula_weight	7838.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N,R,V

MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVK

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	Synaptosomal-associated protein 25
Molecular weight formula_weight	9030.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O,S,W

MRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLGK

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 polymer

Description description	Synaptosomal-associated protein 25
Molecular weight formula_weight	7471.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P,T,X

MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG

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 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	10

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Resolution resolution	10.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	2082

Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+

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

Synaptotagmin-1

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6mti__assembly_1__model_1

6mti__assembly_1__model_1 | I(q)

6mti__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)