6QD6: PDB entry 6QD6

Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of Mb-cHopQ-Nb207. Determined by X-ray diffraction at 2.84 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 2.84 Å
Organisms: Helicobacter pylori, Helicobacter pylori (strain G27)
Chains: 10
Atoms: 33,077
Mol. weight: 580.53 kDa
Released: 18 Dec 2019

Explore 6QD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QD6 contains 182 α-helices and 233 β-strands across 10 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: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-11	2	2
α-helix	12-13	2
β-strand	14-24	11	3
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	4
β-strand	48	1	5
α-helix	49	1
α-helix	66-71	6
β-strand	75	1	4
α-helix	81-106	26
α-helix	109-112	4
α-helix	123-159	37
α-helix	163-166	4
α-helix	195-211	17
α-helix	213-217	5
α-helix	220-229	10
α-helix	273-292	20
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	5
β-strand	323	1	6
β-strand	326	1	7
β-strand	337-341	5	3
α-helix	343-345	3
β-strand	347-351	5	3
β-strand	371	1	7
β-strand	378	1	6
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	3
β-strand	424-430	7	1
β-strand	439-445	7	2
β-strand	452-458	7	2
β-strand	464-466	3	2
β-strand	474-479	6	1
β-strand	484-489	6	1
α-helix	494-496	3
β-strand	498-505	8	2
α-helix	512-513	2
α-helix	516-518	3
β-strand	521-522	2	2
β-strand	526-529	4	2

Chain B: 17 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-11	2	9
α-helix	12-13	2
β-strand	14-24	11	3
α-helix	27-44	18
β-strand	47	1	10
β-strand	48	1	11
α-helix	49	1
α-helix	66-71	6
β-strand	72	1	11
β-strand	75	1	10
α-helix	76-106	31
α-helix	123-159	37
β-strand	179-180	2	3
α-helix	195-210	16
α-helix	213-225	13
α-helix	277-292	16
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	11
β-strand	323	1	12
β-strand	326	1	13
β-strand	336-341	6	3
β-strand	347-352	6	3
β-strand	371	1	13
β-strand	373	1	14
β-strand	377	1	14
β-strand	378	1	12
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	3
β-strand	424-430	7	8
α-helix	431	1
β-strand	439-445	7	9
β-strand	452-458	7	9
β-strand	463-466	4	9
β-strand	474-479	6	8
β-strand	484-489	6	8
α-helix	494-496	3
β-strand	498-505	8	9
α-helix	516-518	3
β-strand	521-522	2	9
β-strand	526-529	4	9

Chain C: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-11	2	16
α-helix	12-13	2
β-strand	14-24	11	17
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	18
β-strand	48	1	19
α-helix	49	1
α-helix	66-71	6
β-strand	75	1	18
α-helix	77-106	30
α-helix	127-158	32
β-strand	179-181	3	17
α-helix	195-210	16
α-helix	213-216	4
α-helix	277-292	16
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	19
β-strand	323	1	20
β-strand	326	1	21
β-strand	336-341	6	17
β-strand	347-352	6	17
β-strand	371	1	21
β-strand	373	1	22
β-strand	377	1	22
β-strand	378	1	20
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	17
β-strand	424-430	7	15
α-helix	431	1
β-strand	439-445	7	16
β-strand	452-458	7	16
β-strand	463-466	4	16
β-strand	474-479	6	15
β-strand	484-489	6	15
α-helix	494-496	3
β-strand	498-505	8	16
α-helix	512-513	2
α-helix	516-518	3
β-strand	521-522	2	16
β-strand	526-529	4	16

Chain D: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	23
β-strand	10-11	2	24
α-helix	12-13	2
β-strand	14-24	11	17
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	25
β-strand	48	1	26
α-helix	66-71	6
β-strand	75	1	25
α-helix	76-105	30
α-helix	109-111	3
α-helix	123-159	37
α-helix	195-210	16
α-helix	213-229	17
α-helix	273-292	20
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	26
β-strand	323	1	27
β-strand	326	1	28
β-strand	336-341	6	17
β-strand	347-352	6	17
β-strand	371	1	28
β-strand	373	1	29
β-strand	377	1	29
β-strand	378	1	27
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	17
β-strand	424-428	5	23
β-strand	439-445	7	24
α-helix	450-451	2
β-strand	452-457	6	24
β-strand	464-466	3	24
α-helix	468-470	3
β-strand	474-479	6	23
β-strand	484-489	6	23
α-helix	494-496	3
β-strand	498-505	8	24
α-helix	512-513	2
α-helix	516-518	3
β-strand	521-522	2	24
β-strand	526-529	4	24

Chain E: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	30
β-strand	10-11	2	31
α-helix	12-13	2
β-strand	14-24	11	32
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	33
β-strand	48	1	34
α-helix	49	1
α-helix	66-71	6
β-strand	72	1	34
β-strand	75	1	33
α-helix	76-106	31
α-helix	109-111	3
α-helix	123-159	37
β-strand	179-181	3	32
α-helix	195-211	17
α-helix	214-223	10
α-helix	275-292	18
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	34
β-strand	323	1	35
β-strand	326	1	36
β-strand	337-341	5	32
β-strand	347-351	5	32
α-helix	370	1
β-strand	371	1	36
α-helix	372	1
β-strand	378	1	35
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	32
β-strand	424-430	7	30
β-strand	439-445	7	31
β-strand	451-458	8	31
β-strand	464-466	3	31
β-strand	474-479	6	30
β-strand	484-489	6	30
α-helix	494-496	3
β-strand	498-505	8	31
α-helix	512-513	2
β-strand	521-522	2	31
β-strand	526-529	4	31

Chain F: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	10-11	2	38
α-helix	12-13	2
β-strand	14-24	11	32
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	39
β-strand	48	1	40
α-helix	49	1
α-helix	66-71	6
β-strand	75	1	39
α-helix	76-106	31
β-strand	117	1	41
α-helix	123-159	37
α-helix	195-210	16
α-helix	213-227	15
α-helix	253-259	7
α-helix	273-292	20
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	40
β-strand	323	1	42
β-strand	326	1	43
β-strand	336-340	5	32
β-strand	348-352	5	32
β-strand	371	1	43
β-strand	378	1	42
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	32
β-strand	424-430	7	37
α-helix	431	1
β-strand	439-445	7	38
β-strand	452-458	7	38
β-strand	463-466	4	38
β-strand	474-479	6	37
β-strand	484-489	6	37
α-helix	494-496	3
β-strand	498-505	8	38
α-helix	516-518	3
β-strand	521-522	2	38
β-strand	526-529	4	38

Chain G: 17 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	44
β-strand	10-11	2	41
α-helix	12-13	2
β-strand	14-24	11	45
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	46
β-strand	48	1	47
α-helix	66-71	6
β-strand	72	1	47
β-strand	75	1	46
α-helix	76-106	31
α-helix	109-112	4
α-helix	123-159	37
β-strand	179-180	2	45
α-helix	195-228	34
α-helix	253-258	6
α-helix	276-292	17
α-helix	298-317	20
α-helix	318-320	3
β-strand	321	1	47
β-strand	323	1	48
β-strand	326	1	49
β-strand	336-341	6	45
β-strand	347-352	6	45
β-strand	371	1	49
β-strand	373	1	50
β-strand	377	1	50
β-strand	378	1	48
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	45
β-strand	424-430	7	44
β-strand	439-445	7	41
β-strand	451-458	8	41
β-strand	463-466	4	41
β-strand	474-479	6	44
β-strand	484-489	6	44
α-helix	494-496	3
β-strand	498-505	8	41
α-helix	516-518	3
β-strand	521-522	2	41
β-strand	526-529	4	41

Chain H: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	51
β-strand	10-11	2	52
α-helix	12-13	2
β-strand	14-24	11	45
α-helix	27-44	18
α-helix	46	1
β-strand	47	1	53
β-strand	48	1	54
α-helix	49	1
β-strand	75	1	53
α-helix	76-105	30
α-helix	123-158	36
α-helix	195-210	16
α-helix	213-230	18
α-helix	273-292	20
α-helix	298-317	20
β-strand	321	1	54
β-strand	323	1	55
β-strand	336-339	4	45
β-strand	349-352	4	45
β-strand	373	1	56
β-strand	377	1	56
β-strand	378	1	55
α-helix	380-395	16
α-helix	396-400	5
α-helix	402-404	3
β-strand	411-421	11	45
β-strand	424-427	4	51
β-strand	439-445	7	52
β-strand	451-458	8	52
β-strand	463-466	4	52
β-strand	474-479	6	51
β-strand	484-489	6	51
α-helix	494-496	3
β-strand	498-503	6	52
β-strand	527-529	3	52

2 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
Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207	A, B, C, D, E, F, G, H, I, J	protein	542	Helicobacter pylori, Helicobacter pylori (strain G27)	B5Z8H1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>6QD6_1 Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207 (chains A, B, C, D, E, F, G, H, I, J)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTN
NANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNL
NSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMT
MQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRASGG
GSGGGGSGKLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAY
QATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNG
THSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSK
YGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDN
AKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSHHHHHHEP
EA

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. DOI 10.1038/s41592-020-01001-6

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…
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…

Browse structure collections

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