6BY7 | pdb_00006by7

Folding DNA into a lipid-conjugated nano-barrel for controlled reconstitution of membrane proteins

• PDB DOI: https://doi.org/10.2210/pdb6BY7/pdb
• NAKB: 6BY7
• EM Map EMD-7304: EMDB EMDataResource

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-12-20 Released: 2018-02-28 
• Deposition Author(s): Dong, Y., Chen, S., Zhang, S., Sodroski, J., Yang, Z., Liu, D., Mao, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins.

Dong, Y., Chen, S., Zhang, S., Sodroski, J., Yang, Z., Liu, D., Mao, Y.

(2018) Angew Chem Int Ed Engl 57: 2072-2076

• PubMed: 29266648 
• DOI: https://doi.org/10.1002/anie.201710147
• Primary Citation Related Structures: 
  6BY7


• PubMed Abstract: 
  

  Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared with the membrane-scaffolding-protein nanodisc technique, our approach gives rise to defined stoichiometry, controlled sizes, as well as enhanced stability and homogeneity in membrane protein reconstitution. We further demonstrate potential applications of the DNA nanobarrels in the structural analysis of membrane proteins.

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Organizational Affiliation: 
• Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, and Center for Quantitative Biology, Peking University, Beijing, 100871, China.
Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 2,715.22 kDa 
• Atom Count: 180,167 
• Modeled Residue Count: 8,803 
• Deposited Residue Count: 8,803 
• Unique nucleic acid chains: 118

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (52-MER)	A [auth 1A]	52	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (55-MER)	B [auth 1B]	55	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*AP*CP*GP*GP*CP*TP*CP*AP*GP*AP*GP*C)-3')	C [auth 1C]	16	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (59-MER)	D [auth 1D]	59	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (51-MER)	E [auth 1E]	51	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (46-MER)	F [auth 1F]	46	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*AP*CP*CP*GP*AP*GP*CP*TP*TP*GP*CP*TP*T)-3')	G [auth 1G]	16	synthetic construct

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	H [auth 1H]	48	synthetic construct

Entity ID: 9
Molecule	Chains	Length	Organism	Image
DNA (47-MER)	I [auth 1I]	47	synthetic construct

Entity ID: 10
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*TP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*TP*TP*TP*TP*AP*TP*TP*AP*CP*A)-3')	J [auth 1J]	24	synthetic construct

Entity ID: 11
Molecule	Chains	Length	Organism	Image
DNA (46-MER)	K [auth 1K]	46	synthetic construct

Entity ID: 12
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*AP*CP*AP*GP*AP*AP*TP*GP*AP*AP*AP*GP*AP*G)-3')	L [auth 1L]	16	synthetic construct

Entity ID: 13
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	M [auth 1M]	32	synthetic construct

Entity ID: 14
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	N [auth 1O]	40	synthetic construct

Entity ID: 15
Molecule	Chains	Length	Organism	Image
DNA (46-MER)	O [auth 1P]	46	synthetic construct

Entity ID: 16
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	P [auth 1Q]	37	synthetic construct

Entity ID: 17
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	Q [auth 1R]	48	synthetic construct

Entity ID: 18
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	R [auth 1S]	37	synthetic construct

Entity ID: 19
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*CP*AP*CP*CP*AP*GP*AP*TP*TP*CP*AP*TP*C)-3')	S [auth 1T]	16	synthetic construct

Entity ID: 20
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	T [auth 1U]	40	synthetic construct

Entity ID: 21
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	U [auth 1V]	26	synthetic construct

Entity ID: 22
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	V [auth 1W]	40	synthetic construct

Entity ID: 23
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	W [auth 1X]	48	synthetic construct

Entity ID: 24
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	X [auth 1Y]	27	synthetic construct

Entity ID: 25
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	Y [auth 1Z]	26	synthetic construct

Entity ID: 26
Molecule	Chains	Length	Organism	Image
DNA (47-MER)	Z [auth 1a]	47	synthetic construct

Entity ID: 27
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	AA [auth 1b]	32	synthetic construct

Entity ID: 28
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	BA [auth 1c]	40	synthetic construct

Entity ID: 29
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	CA [auth 1d]	40	synthetic construct

Entity ID: 30
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	DA [auth 1e]	26	synthetic construct

Entity ID: 31
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	EA [auth 1f]	40	synthetic construct

Entity ID: 32
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	FA [auth 1g]	48	synthetic construct

Entity ID: 33
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	GA [auth 1h]	48	synthetic construct

Entity ID: 34
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	HA [auth 1i]	48	synthetic construct

Entity ID: 35
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	IA [auth 1j]	32	synthetic construct

Entity ID: 36
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	JA [auth 1k]	40	synthetic construct

Entity ID: 37
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	KA [auth 1l]	48	synthetic construct

Entity ID: 38
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*GP*AP*GP*GP*TP*GP*AP*TP*TP*CP*GP*CP*GP*T)-3')	LA [auth 1m]	16	synthetic construct

Entity ID: 39
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	MA [auth 1n]	56	synthetic construct

Entity ID: 40
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	NA [auth 1o]	40	synthetic construct

Entity ID: 41
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	OA [auth 1p]	40	synthetic construct

Entity ID: 42
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	PA [auth 1q]	48	synthetic construct

Entity ID: 43
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	QA [auth 1r]	32	synthetic construct

Entity ID: 44
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	RA [auth 1s]	32	synthetic construct

Entity ID: 45
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	SA [auth 1t]	32	synthetic construct

Entity ID: 46
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	TA [auth 1u]	48	synthetic construct

Entity ID: 47
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*CP*CP*CP*AP*GP*CP*TP*GP*GP*TP*CP*AP*TP*A)-3')	UA [auth 1v]	16	synthetic construct

Entity ID: 48
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	VA [auth 1w]	40	synthetic construct

Entity ID: 49
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*CP*AP*GP*AP*TP*GP*CP*GP*TP*GP*CP*CP*AP*G)-3')	WA [auth 1x]	16	synthetic construct

Entity ID: 50
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	XA [auth 2N]	36	synthetic construct

Entity ID: 51
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	YA [auth 2A]	32	synthetic construct

Entity ID: 52
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	ZA [auth 2B]	48	synthetic construct

Entity ID: 53
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	AB [auth 2C]	26	synthetic construct

Entity ID: 54
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	BB [auth 2D]	32	synthetic construct

Entity ID: 55
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*TP*AP*AP*CP*GP*CP*AP*TP*AP*AP*AP*AP*CP*GP*AP*GP*GP*AP*GP*GP*TP*T)-3')	CB [auth 2E]	40	synthetic construct

Entity ID: 56
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	DB [auth 2F]	48	synthetic construct

Entity ID: 57
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	EB [auth 2G]	40	synthetic construct

Entity ID: 58
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	FB [auth 2H]	40	synthetic construct

Entity ID: 59
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	GB [auth 2I]	16	synthetic construct

Entity ID: 60
Molecule	Chains	Length	Organism	Image
DNA (58-MER)	HB [auth 2J]	29	synthetic construct

Entity ID: 61
Molecule	Chains	Length	Organism	Image
DNA (52-MER)	IB [auth 2K]	24	synthetic construct

Entity ID: 62
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	JB [auth 2L]	32	synthetic construct

Entity ID: 63
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	KB [auth 2M]	24	synthetic construct

Entity ID: 64
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	LB [auth 2O]	26	synthetic construct

Entity ID: 65
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	MB [auth 2P]	40	synthetic construct

Entity ID: 66
Molecule	Chains	Length	Organism	Image
DNA (58-MER)	NB [auth 2Q]	40	synthetic construct

Entity ID: 67
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	OB [auth 2R]	40	synthetic construct

Entity ID: 68
Molecule	Chains	Length	Organism	Image
DNA (52-MER)	PB [auth 2S]	58	synthetic construct

Entity ID: 69
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	QB [auth 2T]	24	synthetic construct

Entity ID: 70
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	RB [auth 2U]	52	synthetic construct

Entity ID: 71
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	SB [auth 2V]	40	synthetic construct

Entity ID: 72
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	TB [auth 2W]	48	synthetic construct

Entity ID: 73
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	UB [auth 2X]	48	synthetic construct

Entity ID: 74
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	VB [auth 2Y]	32	synthetic construct

Entity ID: 75
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	WB [auth 2Z]	40	synthetic construct

Entity ID: 76
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*GP*TP*TP*AP*AP*AP*AP*CP*CP*GP*AP*TP*A)-3')	XB [auth 2a]	58	synthetic construct

Entity ID: 77
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	YB [auth 2b]	56	synthetic construct

Entity ID: 78
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	ZB [auth 2c]	45	synthetic construct

Entity ID: 79
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	AC [auth 2d]	52	synthetic construct

Entity ID: 80
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*GP*CP*CP*TP*TP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*AP*AP*AP*AP*TP*A)-3')	BC [auth 2e]	37	synthetic construct

Entity ID: 81
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	CC [auth 2f]	48	synthetic construct

Entity ID: 82
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	DC [auth 2g]	48	synthetic construct

Entity ID: 83
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	EC [auth 2h]	56	synthetic construct

Entity ID: 84
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	FC [auth 2i]	32	synthetic construct

Entity ID: 85
Molecule	Chains	Length	Organism	Image
DNA (47-MER)	GC [auth 2j]	16	synthetic construct

Entity ID: 86
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*GP*TP*GP*CP*CP*AP*AP*AP*TP*CP*CP*GP*C)-3')	HC [auth 2k]	32	synthetic construct

Entity ID: 87
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	IC [auth 2l]	48	synthetic construct

Entity ID: 88
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	JC [auth 2m]	48	synthetic construct

Entity ID: 89
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	KC [auth 2n]	16	synthetic construct

Entity ID: 90
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	LC [auth 2o]	32	synthetic construct

Entity ID: 91
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	MC [auth 2p]	32	synthetic construct

Entity ID: 92
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	NC [auth 2q]	40	synthetic construct

Entity ID: 93
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	OC [auth 2r]	24	synthetic construct

Entity ID: 94
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	PC [auth 2s]	32	synthetic construct

Entity ID: 95
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	QC [auth 2t]	40	synthetic construct

Entity ID: 96
Molecule	Chains	Length	Organism	Image
DNA (55-MER)	RC [auth 2u]	32	synthetic construct

Entity ID: 97
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	SC [auth 2v]	32	synthetic construct

Entity ID: 98
Molecule	Chains	Length	Organism	Image
DNA (38-MER)	TC [auth 2w]	47	synthetic construct

Entity ID: 99
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	UC [auth 2x]	16	synthetic construct

Entity ID: 100
Molecule	Chains	Length	Organism	Image
DNA (4346-MER)	VC [auth 3N]	4,346	synthetic construct

Entity ID: 101
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	WC [auth 3A]	40	synthetic construct

Entity ID: 102
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	XC [auth 3B]	40	synthetic construct

Entity ID: 103
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	YC [auth 3C]	48	synthetic construct

Entity ID: 104
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	ZC [auth 3D]	48	synthetic construct

Entity ID: 105
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	AD [auth 3E]	48	synthetic construct

Entity ID: 106
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	BD [auth 3F]	56	synthetic construct

Entity ID: 107
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*AP*GP*GP*AP*TP*AP*TP*TP*C)-3')	CD [auth 3G]	16	synthetic construct

Entity ID: 108
Molecule	Chains	Length	Organism	Image
DNA (56-MER)	DD [auth 3H]	56	synthetic construct

Entity ID: 109
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	ED [auth 3I]	36	synthetic construct

Entity ID: 110
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	FD [auth 3J]	35	synthetic construct

Entity ID: 111
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	GD [auth 3S]	32	synthetic construct

Entity ID: 112
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	HD [auth 3K]	48	synthetic construct

Entity ID: 113
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	ID [auth 3L]	37	synthetic construct

Entity ID: 114
Molecule	Chains	Length	Organism	Image
DNA (55-MER)	JD [auth 3M]	55	synthetic construct

Entity ID: 115
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	KD [auth 3O]	48	synthetic construct

Entity ID: 116
Molecule	Chains	Length	Organism	Image
DNA (38-MER)	LD [auth 3P]	38	synthetic construct

Entity ID: 117
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	MD [auth 3Q]	26	synthetic construct

Entity ID: 118
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	ND [auth 3R]	32	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Dong, Y., Chen, S., Zhang, S., Sodroski, J., Yang, Z., Liu, D., Mao, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	11774012
National Natural Science Foundation of China (NSFC)	China	91530321
National Natural Science Foundation of China (NSFC)	China	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI93256
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI24982
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100645
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI24755

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references