6XV8: Megabody Mb-Nb207-c7HopQ_G10

Crystal structure of Megabody Mb-Nb207-c7HopQ_G10. Determined by X-ray diffraction at 3.15 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Lama glama, Helicobacter pylori (strain G27)
Chains: 4
Atoms: 12,431
Mol. weight: 224.66 kDa
Released: 13 Jan 2021

Explore 6XV8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XV8 contains 62 α-helices and 77 β-strands across 4 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: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	12-23	12	1
α-helix	26-43	18
β-strand	46	1	2
α-helix	66-70	5
β-strand	74	1	2
α-helix	75-105	31
α-helix	127-157	31
α-helix	194-210	17
α-helix	212-217	6
α-helix	257-272	16
α-helix	278-297	20
α-helix	298-300	3
β-strand	303	1	3
β-strand	317-318	2	1
β-strand	331	1	1
β-strand	358	1	3
α-helix	360-375	16
α-helix	376-380	5
α-helix	382-384	3
β-strand	391-408	18	1
β-strand	418-424	7	4
β-strand	431-437	7	4
β-strand	442-445	4	4
α-helix	447-449	3
β-strand	453-458	6	1
β-strand	463-469	7	1
β-strand	478-484	7	4
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	4
β-strand	505-506	2	4

Chain B: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
β-strand	8	1	5
β-strand	12-23	12	5
α-helix	26-43	18
β-strand	46	1	6
α-helix	65-70	6
β-strand	74	1	6
α-helix	75-105	31
α-helix	124-127	4
α-helix	128-157	30
α-helix	162-166	5
α-helix	194-209	16
α-helix	212-220	9
α-helix	254-272	19
α-helix	280-297	18
β-strand	303	1	7
β-strand	306	1	8
β-strand	317-321	5	5
β-strand	327-331	5	5
β-strand	351	1	8
β-strand	353	1	9
β-strand	357	1	9
β-strand	358	1	7
α-helix	360-379	20
α-helix	382-384	3
β-strand	391-408	18	5
α-helix	414-416	3
β-strand	418-424	7	10
β-strand	431-437	7	10
β-strand	442-445	4	10
α-helix	447-449	3
β-strand	453-458	6	5
β-strand	463-469	7	5
α-helix	473-475	3
β-strand	477-484	8	10
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	10
β-strand	505-507	3	10

Chain C: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	5-22	18	5
α-helix	26-43	18
α-helix	45-46	2
β-strand	47	1	12
α-helix	65-70	6
α-helix	75-105	31
α-helix	124-126	3
α-helix	128-156	29
α-helix	194-209	16
α-helix	214-217	4
α-helix	256-272	17
α-helix	280-297	18
α-helix	298-300	3
β-strand	301	1	12
β-strand	303	1	13
β-strand	306	1	14
β-strand	317-319	3	5
β-strand	329-331	3	5
β-strand	351	1	14
β-strand	358	1	13
α-helix	360-378	19
α-helix	382-384	3
β-strand	392-408	17	5
β-strand	418-424	7	15
β-strand	431-435	5	15
β-strand	444-445	2	15
α-helix	447-449	3
β-strand	453-458	6	5
β-strand	463-468	6	5
α-helix	473-475	3
β-strand	477-484	8	15
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	15
β-strand	502	1	11
β-strand	505-507	3	15

Chain D: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	16
β-strand	12-23	12	16
α-helix	26-43	18
β-strand	46	1	17
α-helix	65-70	6
β-strand	74	1	17
α-helix	75-104	30
α-helix	130-157	28
α-helix	194-206	13
α-helix	211-215	5
α-helix	255-271	17
α-helix	278-297	20
α-helix	298-300	3
β-strand	303	1	18
β-strand	317-318	2	16
β-strand	320	1	19
β-strand	328	1	19
β-strand	358	1	18
α-helix	360-378	19
α-helix	382-384	3
β-strand	391-408	18	16
β-strand	419-424	6	20
β-strand	431-437	7	20
β-strand	442-445	4	20
β-strand	454-458	5	16
β-strand	463-469	7	16
α-helix	473-475	3
β-strand	477-483	7	20
α-helix	495-497	3
β-strand	500-501	2	20
β-strand	505-507	3	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein	A, B, C, D	protein	521	Lama glama, Helicobacter pylori (strain G27)	B5Z8H1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6XV8_1 Outer membrane protein (chains A, B, C, D)
QVQLVESGGGLVLKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNN
ANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLN
SPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTM
QNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSRL
LTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYA
VICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSI
EQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKSSLRLSCAASGRTFSTAAMG
WFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYY
CAARRRGFTLAPTRANEYDYWGQGTQVTVSSHHHHHHEPEA

Primary citation

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Uchanski, T., Masiulis, S., Fischer, B. et al. Nat Methods (2021) 18:60-68. DOI 10.1038/s41592-020-01001-6 · PubMed

Other PDB entries of the same protein (UniProt B5Z8H1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QFA 2.49 Å, CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody…
9FFU 2.5 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
6XVI 2.6 Å, Crystal structure of Megabody Mb-Nb207-c7HopQ_A12
5LP2 2.6 Å, Adhesin domain of the type 1 HopQ of Helicobacter pylori strain G27
9FAJ 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…
6GBG 2.8 Å, Helicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1
9FFL 2.8 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
6QD6 2.84 Å, Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal…
7QHA 2.97 Å, Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM…
9FFM 3.0 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with Mb25 in the…
9UOK 3.05 Å, Structure of the complex of LGR4_ECD with Norrin
9FFN 3.1 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…

Browse structure collections

About this viewer

MolViewer shows 6XV8 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.