6VFE: Gasdermin D pore

Gasdermin D pore. Determined by electron microscopy at 3.9 Å resolution. Released 21 Apr 2021.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 33
Atoms: 61,908
Mol. weight: 886.06 kDa
Released: 21 Apr 2021

Explore 6VFE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VFE contains 199 α-helices and 480 β-strands across 33 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	3
α-helix	29-31	3
β-strand	38-42	5	3
α-helix	43-45	3
β-strand	55-60	6	3
β-strand	65	1	5
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	3
α-helix	127-136	10
β-strand	139	1	5
α-helix	148-153	6
α-helix	155	1
β-strand	156-166	11	3
β-strand	170-185	16	3
β-strand	194-208	15	3
α-helix	209	1
β-strand	212-220	9	3
β-strand	221-223	3	6
β-strand	227-229	3	6

Chain A: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	1
α-helix	28-31	4
β-strand	38-42	5	1
α-helix	43-45	3
β-strand	55-60	6	1
β-strand	65	1	2
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	1
α-helix	127-136	10
β-strand	139	1	2
α-helix	148-153	6
β-strand	156-165	10	1
β-strand	170-185	16	3
β-strand	193-208	16	3
α-helix	209	1
β-strand	213-220	8	1
β-strand	221-223	3	4
β-strand	227-229	3	4

Chain b: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	10
α-helix	28-31	4
β-strand	38-42	5	10
α-helix	43-45	3
β-strand	55-60	6	10
β-strand	65	1	11
β-strand	80-96	17	3
β-strand	104-120	17	3
β-strand	123-124	2	10
α-helix	127-136	10
β-strand	139	1	11
α-helix	148-153	6
β-strand	156-166	11	10
β-strand	170-180	11	3
β-strand	183-184	2	3
β-strand	194-208	15	3
α-helix	209	1
β-strand	212-220	9	10
β-strand	221-223	3	12
β-strand	227-229	3	12

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	7
α-helix	28-31	4
β-strand	38-42	5	7
α-helix	43-45	3
β-strand	55-60	6	7
β-strand	65	1	8
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	7
α-helix	127-136	10
β-strand	139	1	8
α-helix	148-153	6
β-strand	156-166	11	7
β-strand	170-181	12	3
β-strand	183-185	3	3
β-strand	193-208	16	3
α-helix	209	1
β-strand	212-220	9	7
β-strand	221-223	3	9
β-strand	227-229	3	9

Chain c: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	15
α-helix	28-30	3
β-strand	38-42	5	15
α-helix	43-45	3
β-strand	55-60	6	15
β-strand	65	1	16
β-strand	80-96	17	3
β-strand	104-120	17	3
β-strand	123-124	2	15
α-helix	127-136	10
β-strand	139	1	16
α-helix	148-153	6
β-strand	156-166	11	15
β-strand	170-180	11	3
β-strand	183-184	2	3
β-strand	193-208	16	3
α-helix	209	1
β-strand	212-220	9	15
β-strand	221-223	3	17
β-strand	227-229	3	17

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	13
α-helix	28-31	4
β-strand	38-42	5	13
α-helix	43-45	3
α-helix	51-54	4
β-strand	55-60	6	13
β-strand	65	1	14
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	13
α-helix	127-136	10
β-strand	139	1	14
α-helix	148-153	6
β-strand	156-166	11	13
β-strand	170-185	16	3
β-strand	194-208	15	3
α-helix	209	1
β-strand	212-223	12	13
β-strand	227-230	4	13

Chain d: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	21
α-helix	28-31	4
β-strand	38-42	5	21
α-helix	43-45	3
β-strand	55-60	6	21
β-strand	65	1	22
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	21
α-helix	127-136	10
β-strand	139	1	22
α-helix	148-153	6
α-helix	155	1
β-strand	156-166	11	21
β-strand	170-185	16	3
β-strand	193-208	16	3
β-strand	212-220	9	21
β-strand	221-223	3	23
β-strand	227-229	3	23

Chain D: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	23-24	2	18
α-helix	28-33	6
β-strand	38-42	5	18
α-helix	43-45	3
β-strand	55-60	6	18
β-strand	65	1	19
β-strand	80-96	17	3
β-strand	103-120	18	3
β-strand	123-124	2	18
α-helix	127-136	10
β-strand	139	1	19
α-helix	148-153	6
β-strand	156-166	11	18
β-strand	170-185	16	3
β-strand	193-208	16	3
α-helix	209	1
β-strand	212-220	9	18
β-strand	221-223	3	20
β-strand	227-229	3	20

23 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gasdermin-D, N-terminal	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g	protein	241	Homo sapiens	P57764 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g), FASTA

>6VFE_1 Gasdermin-D, N-terminal (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g)
MGSAFERVVRRVVQELDHGGEFIPVTSLQSSTGFQPYCLVVRKPSSSWFWKPRYKCVNLS
IKDILEPDAAEPDVQRGRSFHFYDAMDGQIQGSVELAAPGQAKIAGGAAVSDSSSTSMNV
YSLSVDPNTWQTLLHERHLRQPEHKVLQQLRSRGDNVYVVTEVLQTQKEVEVTRTHKREG
SGRFSLPGATCEQGEGQGHLSQKKTVTIPSGSTLAFRVAQLVIDSDLDVLLFPDKKQRTF
Q

Primary citation

Gasdermin D pore structure reveals preferential release of mature interleukin-1. Xia, S., Zhang, Z., Magupalli, V.G. et al. Nature (2021) 593:607-611. DOI 10.1038/s41586-021-03478-3 · PubMed

Other PDB entries of the same protein (UniProt P57764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E0V 1.64 Å, GSDMD bound to a peptide
7Z1X 1.86 Å, Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6
5NH1 2.04 Å, Structure of the C-terminal domain of human Gasdermin D
5WQT 2.64 Å, Structure of a protein involved in pyroptosis
6KN0 2.79 Å, caspase-1 P20/P10 C285A in complex with human GSDMD-C domain
6AO4 2.9 Å, Crystal structure of the human gasdermin D C-terminal domain
23BD 3.4 Å, Caspase-4 p22/p10 and human GSDMD complex
6N9O 3.5 Å, Crystal structure of human GSDMD
23BB 3.6 Å, Caspase-4 p20/p10 and human GSDMD
6KMZ 3.61 Å, caspase-4 P22/P10 C258A in complex with human GSDMD-C domain

Browse structure collections

About this viewer

MolViewer shows 6VFE 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.