7UDB: Syntaxin-binding protein 1

Cryo-EM structure of a synaptobrevin-Munc18-1-syntaxin-1 complex class 2. Determined by electron microscopy at 3.5 Å resolution. Released 6 Apr 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 6,472
Mol. weight: 104.58 kDa
Released: 6 Apr 2022

Explore 7UDB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UDB contains 42 α-helices and 27 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	15-20	6
β-strand	29-33	5	1
α-helix	35-44	10
α-helix	47-51	5
β-strand	55-60	6	1
β-strand	68	1	2
β-strand	72-77	6	1
α-helix	81-90	10
α-helix	94-96	3
β-strand	99	1	2
β-strand	102-106	5	1
α-helix	109-111	3
α-helix	112-120	9
α-helix	123-126	4
β-strand	127-132	6	1
β-strand	138-139	2	3
β-strand	144-146	3	3
α-helix	152-156	5
α-helix	159-161	3
α-helix	165-183	19
β-strand	188-191	4	3
α-helix	197-215	19
β-strand	229-234	6	3
α-helix	241-243	3
β-strand	248	1	4
α-helix	249-256	8
β-strand	260	1	5
β-strand	263-266	4	5
β-strand	277-280	4	5
α-helix	286-290	5
β-strand	295	1	4
α-helix	296-313	18
α-helix	327-358	32
α-helix	362-374	13
β-strand	376	1	6
α-helix	381	1
β-strand	382	1	6
α-helix	383	1
α-helix	386-394	9
α-helix	401-414	14
α-helix	420-430	11
α-helix	435-437	3
α-helix	438-442	5
α-helix	443-446	4
β-strand	473	1	7
β-strand	476	1	7
α-helix	481-490	10
β-strand	501	1	3
β-strand	536-542	7	3
β-strand	545-546	2	8
α-helix	547-560	14
β-strand	564-569	6	3
β-strand	572-573	2	8
α-helix	575-583	9

Chain B: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	5-11	7
α-helix	31-63	33
α-helix	69-104	36
α-helix	110-148	39
α-helix	163-168	6
α-helix	178-195	18
α-helix	205-222	18
α-helix	233-238	6

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	34-38	5
α-helix	39-73	35
α-helix	74-76	3
α-helix	78	1
β-strand	79	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Syntaxin-binding protein 1	A	protein	607	Rattus norvegicus	P61765 (AlphaFold model)
Syntaxin-1A	B	protein	254	Rattus norvegicus	P32851 (AlphaFold model)
Synaptobrevin-2	C	protein	59	Rattus norvegicus	P63045 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7UDB_1 Syntaxin-binding protein 1 (chains A)
GSPGISGGGGGIHMAPIGLKAVVGEKIMHDVIKKVKKKGEWKVLVVDQLSMRMLSSCCKM
TDIMTEGITIVEDINKRREPLPSLEAVYLITPSEKSVHSLISDFKDPPTAKYRAAHVFFT
DSCPDALFNELVKSRAAKVIKTLTEINIAFLPYESQVYSLDSADSFQSFYSPHKAQMKNP
ILERLAEQIATLCATLKEYPAVRYRGEYKDNALLAQLIQDKLDAYKADDPTMGEGPDKAR
SQLLILDRGFDPSSPVLHELTFQAMSYDLLPIENDVYKYETSGIGEARVKEVLLDEDDDL
WIALRHKHIAEVSQEVTRSLKDFSSSKRMNTGEKTTMRKLSQMLKKMPQYQKELSKYSTH
LHLAEDCMKHYQGTVDKLCRVEQDLAMGTDAEGEKIKDPMRAIVPILLDANVSTYDKIRI
ILLYIFLKNGITEENLNKLIQHAQIPPEDSEIITNMAHLGVPIVTDSTLRRRSKPERKER
ISEQTYQLSRWTPIIKDIMEDTIEDKLDTKHYPYISTRSSASFSTTAVSARYGHWHKNKA
PGEYRSGPRLIIFILGGVSLNEMRCAYEVTQANGKWEVLIGSTHILTPQKLLDTLKKLNK
TDEEISS

Sequence of entity 2 (B), FASTA

>7UDB_2 Syntaxin-1A (chains B)
GSKDRTQELRTAKDSDDDDDVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHS
AILASPNPDEKTKEELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQ
HSTLSRKFVEVMSEYNATQSDYRERAKGRIQRQLEITGRTTTSEEAADMLESGNPAIFAS
GIIMDSSISKQALSEIETRHSEIIKCENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEH
AVDYVERAVSDTKK

Sequence of entity 3 (C), FASTA

>7UDB_3 Synaptobrevin-2 (chains C)
GSMWNRRLQQTCAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAK

Primary citation

SNARE assembly enlightened by cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex. Stepien, K.P., Xu, J., Zhang, X. et al. Sci Adv (2022) 8:eabo5272-eabo5272. DOI 10.1126/sciadv.abo5272 · PubMed

Other PDB entries of the same protein (UniProt P61765 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JEH 2.5 Å, Crystal Structure of Munc18a and Syntaxin1 lacking N-peptide complex
3C98 2.6 Å, Revised structure of the munc18a-syntaxin1 complex
4JEU 3.2 Å, Crystal Structure of Munc18a and Syntaxin1 with native N-terminus complex
7XSJ 3.2 Å, The structure of the Mint1/Munc18-1/syntaxin-1 complex
3PUJ 3.31 Å, Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex
6LPC 3.4 Å, Crystal Structure of rat Munc18-1 with K332E/K333E mutation
7UDC 3.7 Å, cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex class1

Browse structure collections

About this viewer

MolViewer shows 7UDB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.