6XVI: Megabody Mb-Nb207-c7HopQ_A12

Crystal structure of Megabody Mb-Nb207-c7HopQ_A12. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Helicobacter pylori (strain G27), Helicobacter pylori G27
Chains: 4
Atoms: 13,015
Mol. weight: 224.88 kDa
Released: 13 Jan 2021

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

Secondary structure: helices and β-sheets

6XVI contains 68 α-helices and 86 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: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	12-23	12	1
α-helix	26-43	18
α-helix	45	1
β-strand	46	1	2
β-strand	47	1	3
α-helix	48	1
α-helix	65-70	6
β-strand	74	1	2
α-helix	75-104	30
α-helix	121-157	37
α-helix	160-163	4
α-helix	194-210	17
α-helix	212-227	16
α-helix	253-272	20
α-helix	278-297	20
α-helix	298-300	3
β-strand	301	1	3
β-strand	303	1	4
β-strand	306	1	5
β-strand	316-320	5	1
β-strand	328-332	5	1
β-strand	351	1	5
β-strand	353	1	6
β-strand	357	1	6
β-strand	358	1	4
α-helix	360-379	20
α-helix	382-384	3
β-strand	391-409	19	1
β-strand	418-424	7	7
β-strand	431-437	7	7
β-strand	443-445	3	7
β-strand	453-458	6	1
β-strand	463-469	7	1
α-helix	473-475	3
β-strand	477-484	8	7
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	7
β-strand	505-507	3	7

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	12-23	12	8
α-helix	26-43	18
α-helix	45	1
β-strand	46	1	9
β-strand	47	1	10
α-helix	48	1
α-helix	65-70	6
β-strand	74	1	9
α-helix	75-105	31
α-helix	123-157	35
α-helix	194-210	17
α-helix	212-225	14
α-helix	255-272	18
α-helix	278-297	20
α-helix	298-300	3
β-strand	301	1	10
β-strand	303-305	3	11
β-strand	306	1	12
β-strand	316-320	5	8
β-strand	328-332	5	8
β-strand	351	1	12
β-strand	358-359	2	11
α-helix	360-379	20
α-helix	382-384	3
β-strand	391-409	19	8
β-strand	418-424	7	13
β-strand	431-437	7	13
β-strand	443-445	3	13
β-strand	453-458	6	8
β-strand	463-469	7	8
α-helix	473-475	3
β-strand	477-484	8	13
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	13
β-strand	505-507	3	13

Chain C: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	12-23	12	14
α-helix	26-43	18
α-helix	45	1
β-strand	46	1	15
β-strand	47	1	16
α-helix	48	1
α-helix	65-70	6
β-strand	74	1	15
α-helix	75-105	31
α-helix	125-156	32
α-helix	194-210	17
α-helix	213-225	13
α-helix	253-272	20
α-helix	278-297	20
α-helix	298-300	3
β-strand	301	1	16
β-strand	303-305	3	17
β-strand	306	1	18
β-strand	316-321	6	14
β-strand	327-332	6	14
β-strand	351	1	18
β-strand	358-359	2	17
α-helix	360-379	20
α-helix	382-384	3
β-strand	391-409	19	14
β-strand	418-424	7	19
α-helix	429-430	2
β-strand	431-437	7	19
β-strand	443-445	3	19
β-strand	453-458	6	14
β-strand	463-469	7	14
α-helix	473-475	3
β-strand	477-484	8	19
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	19
β-strand	505-507	3	19

Chain D: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	12-23	12	13
α-helix	26-43	18
α-helix	45	1
β-strand	46	1	20
β-strand	47	1	21
α-helix	48	1
α-helix	65-70	6
β-strand	74	1	20
α-helix	75-104	30
α-helix	122-157	36
α-helix	160-163	4
α-helix	194-210	17
α-helix	212-223	12
α-helix	255-272	18
α-helix	278-297	20
α-helix	298-300	3
β-strand	301	1	21
β-strand	303-305	3	22
β-strand	306	1	23
β-strand	316-321	6	13
β-strand	327-332	6	13
β-strand	351	1	23
β-strand	358-359	2	22
α-helix	360-375	16
α-helix	376-380	5
α-helix	382-384	3
β-strand	391-409	19	13
β-strand	418-424	7	8
β-strand	431-437	7	8
β-strand	443-446	4	8
β-strand	453-458	6	13
β-strand	463-469	7	13
α-helix	473-475	3
β-strand	477-484	8	8
α-helix	491-492	2
α-helix	495-497	3
β-strand	500-501	2	8
β-strand	505-507	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein,Outer membrane protein,Mb-Nb207-c7HopQ_A12	A, B, C, D	protein	521	Helicobacter pylori (strain G27), Helicobacter pylori G27	B5Z8H1 (AlphaFold model)

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

>6XVI_1 Outer membrane protein,Outer membrane protein,Mb-Nb207-c7HopQ_A12 (chains A, B, C, D)
QVQLVESGGGLVRKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNN
ANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLN
SPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTM
QNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSRL
LTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYA
VICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSI
EQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKPSLRLSCAASGRTFSTAAMG
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…
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…
9FFQ 3.1 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…

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