7ARV | pdb_00007arv

TwistTower_native-twist

PDB DOI: https://doi.org/10.2210/pdb7ARV/pdb
EM Map EMD-11379: EMDB EMDataResource
NAKB: 7ARV

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

Deposited: 2020-10-26 Released: 2020-11-18
Deposition Author(s): Kube, M., Kohler, F., Feigl, E., Nagel-Yuksel, B., Willner, E.M., Funke, J.J., Gerling, T., Stommer, P., Honemann, M.N., Martin, T.G., Scheres, S.H.W., Dietz, H.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.

Kube, M., Kohler, F., Feigl, E., Nagel-Yuksel, B., Willner, E.M., Funke, J.J., Gerling, T., Stommer, P., Honemann, M.N., Martin, T.G., Scheres, S.H.W., Dietz, H.

(2020) Nat Commun 11: 6229-6229

PubMed: 33277481 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-20020-7
Primary Citation Related Structures:
7ARE, 7ARQ, 7ART, 7ARV, 7ARY, 7AS5

PubMed Abstract:
The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.

Organizational Affiliation

Physik Department, Technische Universität München, Garching, Germany.

Macromolecule Content

Total Structure Weight: 5,164.34 kDa
Atom Count: 342,569
Modeled Residue Count: 16,756
Deposited Residue Count: 16,756
Unique nucleic acid chains: 195

Macromolecules

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Molecule	Chains	Length	Organism
Entity ID: 1
SCAFFOLD STRAND	A [auth AA]	8,064	synthetic construct
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Entity ID: 2
STAPLE STRAND	B [auth AB]	29	synthetic construct
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Entity ID: 3
STAPLE STRAND	C [auth AC]	48	synthetic construct
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Entity ID: 4
STAPLE STRAND	D [auth AD]	53	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 5
STAPLE STRAND	E [auth AE]	60	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 6
STAPLE STRAND	F [auth AF]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 7
STAPLE STRAND	G [auth AG]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 8
STAPLE STRAND	H [auth AH]	60	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 9
STAPLE STRAND	I [auth AI]	42	synthetic construct
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Entity ID: 10
STAPLE STRAND	J [auth AJ]	60	synthetic construct
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Entity ID: 11
STAPLE STRAND	K [auth AK]	32	synthetic construct
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Entity ID: 12
STAPLE STRAND	L [auth AL]	40	synthetic construct
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Entity ID: 13
STAPLE STRAND	M [auth AM]	48	synthetic construct
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Entity ID: 14
STAPLE STRAND	N [auth AN]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 15
STAPLE STRAND	O [auth AO]	48	synthetic construct
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Entity ID: 16
STAPLE STRAND	P [auth AP]	40	synthetic construct
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Entity ID: 17
STAPLE STRAND	Q [auth AQ]	45	synthetic construct
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Entity ID: 18
STAPLE STRAND	R [auth AR]	48	synthetic construct
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Entity ID: 19
STAPLE STRAND	S [auth AS]	48	synthetic construct
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Entity ID: 20
STAPLE STRAND	T [auth AT]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 21
STAPLE STRAND	U [auth AU]	48	synthetic construct
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Entity ID: 22
STAPLE STRAND	V [auth AV]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 23
STAPLE STRAND	W [auth AW]	58	synthetic construct
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Entity ID: 24
STAPLE STRAND	X [auth AX]	60	synthetic construct
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Entity ID: 25
STAPLE STRAND	Y [auth AY]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 26
STAPLE STRAND	Z [auth AZ]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 27
STAPLE STRAND	AA [auth Aa]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 28
STAPLE STRAND	BA [auth Ab]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 29
STAPLE STRAND	CA [auth Ac]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 30
STAPLE STRAND	DA [auth Ad]	53	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 31
STAPLE STRAND	EA [auth Ae]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 32
STAPLE STRAND	FA [auth Af]	32	synthetic construct
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Entity ID: 33
STAPLE STRAND	GA [auth Ag]	58	synthetic construct
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Entity ID: 34
STAPLE STRAND	HA [auth Ah]	60	synthetic construct
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Entity ID: 35
STAPLE STRAND	IA [auth Ai]	48	synthetic construct
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Entity ID: 36
STAPLE STRAND	JA [auth Aj]	48	synthetic construct
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Entity ID: 37
STAPLE STRAND	KA [auth Ak]	32	synthetic construct
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Entity ID: 38
STAPLE STRAND	LA [auth Al]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 39
STAPLE STRAND	MA [auth Am]	58	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 40
STAPLE STRAND	NA [auth An]	60	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 41
STAPLE STRAND	OA [auth Ao]	57	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 42
STAPLE STRAND	PA [auth Ap]	60	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 43
STAPLE STRAND	QA [auth Aq]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 44
STAPLE STRAND	RA [auth Ar]	37	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 45
STAPLE STRAND	SA [auth As]	40	synthetic construct
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Entity ID: 46
STAPLE STRAND	TA [auth At]	44	synthetic construct
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Entity ID: 47
STAPLE STRAND	UA [auth Au]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 48
STAPLE STRAND	VA [auth Av]	40	synthetic construct
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Entity ID: 49
STAPLE STRAND	WA [auth Aw]	56	synthetic construct
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Entity ID: 50
STAPLE STRAND	XA [auth Ax]	40	synthetic construct
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Entity ID: 51
STAPLE STRAND	YA [auth Ay]	48	synthetic construct
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Entity ID: 52
STAPLE STRAND	ZA [auth Az]	45	synthetic construct
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Entity ID: 53
STAPLE STRAND	AB [auth A0]	32	synthetic construct
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Entity ID: 54
STAPLE STRAND	BB [auth A1]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 55
STAPLE STRAND	CB [auth A2]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 56
STAPLE STRAND	DB [auth A3]	56	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 57
STAPLE STRAND	EB [auth A4]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 58
STAPLE STRAND	FB [auth A5]	48	synthetic construct
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Entity ID: 59
STAPLE STRAND	GB [auth A6]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 60
STAPLE STRAND	HB [auth A7]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 61
STAPLE STRAND	IB [auth A8]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 62
STAPLE STRAND	JB [auth A9]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 63
STAPLE STRAND	KB [auth BA]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 64
STAPLE STRAND	LB [auth BB]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 65
STAPLE STRAND	MB [auth BC]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 66
STAPLE STRAND	NB [auth BD]	57	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 67
STAPLE STRAND	OB [auth BE]	57	synthetic construct
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Entity ID: 68
STAPLE STRAND	PB [auth BF]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 69
STAPLE STRAND	QB [auth BG]	40	synthetic construct
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Entity ID: 70
STAPLE STRAND	RB [auth BH]	57	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 71
STAPLE STRAND	SB [auth BI]	57	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 72
STAPLE STRAND	TB [auth BJ]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 73
STAPLE STRAND	UB [auth BK]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 74
STAPLE STRAND	VB [auth BL]	56	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 75
STAPLE STRAND	WB [auth BM]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 76
STAPLE STRAND	XB [auth BN]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 77
STAPLE STRAND	YB [auth BO]	48	synthetic construct
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Entity ID: 78
STAPLE STRAND	ZB [auth BP]	58	synthetic construct
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Entity ID: 79
STAPLE STRAND	AC [auth BQ]	57	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 80
STAPLE STRAND	BC [auth BR]	48	synthetic construct
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Entity ID: 81
STAPLE STRAND	CC [auth BS]	48	synthetic construct
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Entity ID: 82
STAPLE STRAND	DC [auth BT]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 83
STAPLE STRAND	EC [auth BU]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 84
STAPLE STRAND	FC [auth BV]	58	synthetic construct
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Entity ID: 85
STAPLE STRAND	GC [auth BW]	60	synthetic construct
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Entity ID: 86
STAPLE STRAND	HC [auth BX]	32	synthetic construct
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Entity ID: 87
STAPLE STRAND	IC [auth BY]	40	synthetic construct
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Entity ID: 88
STAPLE STRAND	JC [auth BZ]	40	synthetic construct
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Entity ID: 89
STAPLE STRAND	KC [auth Ba]	48	synthetic construct
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Entity ID: 90
STAPLE STRAND	LC [auth Bb]	48	synthetic construct
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Entity ID: 91
STAPLE STRAND	MC [auth Bc]	32	synthetic construct
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Entity ID: 92
STAPLE STRAND	NC [auth Bd]	48	synthetic construct
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Entity ID: 93
STAPLE STRAND	OC [auth Be]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 94
STAPLE STRAND	PC [auth Bf]	48	synthetic construct
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Entity ID: 95
STAPLE STRAND	QC [auth Bg]	40	synthetic construct
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Entity ID: 96
STAPLE STRAND	RC [auth Bh]	56	synthetic construct
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Entity ID: 97
STAPLE STRAND	SC [auth Bi]	40	synthetic construct
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Entity ID: 98
STAPLE STRAND	TC [auth Bj]	32	synthetic construct
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Entity ID: 99
STAPLE STRAND	UC [auth Bk]	32	synthetic construct
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Entity ID: 100
STAPLE STRAND	VC [auth Bl]	48	synthetic construct
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Entity ID: 101
STAPLE STRAND	WC [auth Bm]	56	synthetic construct
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Entity ID: 102
STAPLE STRAND	XC [auth Bn]	48	synthetic construct
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Entity ID: 103
STAPLE STRAND	YC [auth Bo]	48	synthetic construct
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Entity ID: 104
STAPLE STRAND	ZC [auth Bp]	40	synthetic construct
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Entity ID: 105
STAPLE STRAND	AD [auth Bq]	48	synthetic construct
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Entity ID: 106
STAPLE STRAND	BD [auth Br]	48	synthetic construct
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Entity ID: 107
STAPLE STRAND	CD [auth Bs]	32	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 108
STAPLE STRAND	DD [auth Bt]	40	synthetic construct
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Entity ID: 109
STAPLE STRAND	ED [auth Bu]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 110
STAPLE STRAND	FD [auth Bv]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 111
STAPLE STRAND	GD [auth Bw]	60	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 112
STAPLE STRAND	HD [auth Bx]	45	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 113
STAPLE STRAND	ID [auth By]	40	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 114
STAPLE STRAND	JD [auth Bz]	32	synthetic construct
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Entity ID: 115
STAPLE STRAND	KD [auth B0]	60	synthetic construct
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Entity ID: 116
STAPLE STRAND	LD [auth B1]	60	synthetic construct
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Entity ID: 117
STAPLE STRAND	MD [auth B2]	40	synthetic construct
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Entity ID: 118
STAPLE STRAND	ND [auth B3]	32	synthetic construct
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Entity ID: 119
STAPLE STRAND	OD [auth B4]	32	synthetic construct
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Entity ID: 120
STAPLE STRAND	PD [auth B5]	60	synthetic construct
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Entity ID: 121
STAPLE STRAND	QD [auth B6]	53	synthetic construct
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Entity ID: 122
STAPLE STRAND	RD [auth B7]	48	synthetic construct
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Entity ID: 123
STAPLE STRAND	SD [auth B8]	32	synthetic construct
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Entity ID: 124
STAPLE STRAND	TD [auth B9]	48	synthetic construct
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Entity ID: 125
STAPLE STRAND	UD [auth CA]	48	synthetic construct
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Entity ID: 126
STAPLE STRAND	VD [auth CB]	60	synthetic construct
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Entity ID: 127
STAPLE STRAND	WD [auth CC]	37	synthetic construct
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Entity ID: 128
STAPLE STRAND	XD [auth CD]	57	synthetic construct
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Entity ID: 129
STAPLE STRAND	YD [auth CE]	32	synthetic construct
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Entity ID: 130
STAPLE STRAND	ZD [auth CF]	40	synthetic construct
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Entity ID: 131
STAPLE STRAND	AE [auth CG]	32	synthetic construct
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STAPLE STRAND	BE [auth CH]	53	synthetic construct
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STAPLE STRAND	CE [auth CI]	32	synthetic construct
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STAPLE STRAND	DE [auth CJ]	57	synthetic construct
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STAPLE STRAND	EE [auth CK]	32	synthetic construct
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STAPLE STRAND	FE [auth CL]	40	synthetic construct
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STAPLE STRAND	GE [auth CM]	32	synthetic construct
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STAPLE STRAND	HE [auth CN]	56	synthetic construct
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Entity ID: 139
STAPLE STRAND	IE [auth CO]	48	synthetic construct
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STAPLE STRAND	JE [auth CP]	48	synthetic construct
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Entity ID: 141
STAPLE STRAND	KE [auth CQ]	57	synthetic construct
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Entity ID: 142
STAPLE STRAND	LE [auth CR]	60	synthetic construct
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Entity ID: 143
STAPLE STRAND	ME [auth CS]	48	synthetic construct
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Entity ID: 144
STAPLE STRAND	NE [auth CT]	56	synthetic construct
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Entity ID: 145
STAPLE STRAND	OE [auth CU]	37	synthetic construct
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Entity ID: 146
STAPLE STRAND	PE [auth CV]	32	synthetic construct
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Entity ID: 147
STAPLE STRAND	QE [auth CW]	32	synthetic construct
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Entity ID: 148
STAPLE STRAND	RE [auth CX]	57	synthetic construct
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Entity ID: 149
STAPLE STRAND	SE [auth CY]	60	synthetic construct
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Entity ID: 150
STAPLE STRAND	TE [auth CZ]	48	synthetic construct
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Entity ID: 151
STAPLE STRAND	UE [auth Ca]	48	synthetic construct
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Entity ID: 152
STAPLE STRAND	VE [auth Cb]	40	synthetic construct
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Entity ID: 153
STAPLE STRAND	WE [auth Cc]	32	synthetic construct
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Entity ID: 154
STAPLE STRAND	XE [auth Cd]	40	synthetic construct
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Entity ID: 155
STAPLE STRAND	YE [auth Ce]	40	synthetic construct
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Entity ID: 156
STAPLE STRAND	ZE [auth Cf]	32	synthetic construct
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Entity ID: 157
STAPLE STRAND	AF [auth Cg]	40	synthetic construct
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Entity ID: 158
STAPLE STRAND	BF [auth Ch]	40	synthetic construct
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Entity ID: 159
STAPLE STRAND	CF [auth Ci]	48	synthetic construct
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Entity ID: 160
STAPLE STRAND	DF [auth Cj]	40	synthetic construct
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Entity ID: 161
STAPLE STRAND	EF [auth Ck]	48	synthetic construct
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Entity ID: 162
STAPLE STRAND	FF [auth Cl]	40	synthetic construct
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Entity ID: 163
STAPLE STRAND	GF [auth Cm]	48	synthetic construct
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Entity ID: 164
STAPLE STRAND	HF [auth Cn]	40	synthetic construct
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Entity ID: 165
STAPLE STRAND	IF [auth Co]	40	synthetic construct
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Entity ID: 166
STAPLE STRAND	JF [auth Cp]	37	synthetic construct
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Entity ID: 167
STAPLE STRAND	KF [auth Cq]	37	synthetic construct
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Entity ID: 168
STAPLE STRAND	LF [auth Cr]	40	synthetic construct
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Entity ID: 169
STAPLE STRAND	MF [auth Cs]	40	synthetic construct
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STAPLE STRAND	NF [auth Ct]	45	synthetic construct
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Entity ID: 171
STAPLE STRAND	OF [auth Cu]	37	synthetic construct
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Entity ID: 172
STAPLE STRAND	PF [auth Cv]	40	synthetic construct
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Entity ID: 173
STAPLE STRAND	QF [auth Cw]	40	synthetic construct
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Entity ID: 174
STAPLE STRAND	RF [auth Cx]	32	synthetic construct
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Entity ID: 175
STAPLE STRAND	SF [auth Cy]	32	synthetic construct
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Entity ID: 176
STAPLE STRAND	TF [auth Cz]	32	synthetic construct
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Entity ID: 177
STAPLE STRAND	UF [auth C0]	57	synthetic construct
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Entity ID: 178
STAPLE STRAND	VF [auth C1]	57	synthetic construct
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Entity ID: 179
STAPLE STRAND	WF [auth C2]	32	synthetic construct
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Entity ID: 180
STAPLE STRAND	XF [auth C3]	48	synthetic construct
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Entity ID: 181
STAPLE STRAND	YF [auth C4]	48	synthetic construct
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Entity ID: 182
STAPLE STRAND	ZF [auth C5]	48	synthetic construct
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Entity ID: 183
STAPLE STRAND	AG [auth C6]	48	synthetic construct
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Entity ID: 184
STAPLE STRAND	BG [auth C7]	40	synthetic construct
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Entity ID: 185
STAPLE STRAND	CG [auth C8]	48	synthetic construct
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Entity ID: 186
STAPLE STRAND	DG [auth C9]	57	synthetic construct
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Entity ID: 187
STAPLE STRAND	EG [auth DA]	45	synthetic construct
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Entity ID: 188
STAPLE STRAND	FG [auth DB]	32	synthetic construct
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Entity ID: 189
STAPLE STRAND	GG [auth DC]	40	synthetic construct
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Entity ID: 190
STAPLE STRAND	HG [auth DD]	45	synthetic construct
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Entity ID: 191
STAPLE STRAND	IG [auth DE]	48	synthetic construct
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Entity ID: 192
STAPLE STRAND	JG [auth DF]	40	synthetic construct
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Entity ID: 193
STAPLE STRAND	KG [auth DG]	48	synthetic construct
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Entity ID: 194
STAPLE STRAND	LG [auth DH]	32	synthetic construct
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Entity ID: 195
STAPLE STRAND	MG [auth DI]	32	synthetic construct
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Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 7.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2
RECONSTRUCTION	RELION	3

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--
European Research Council (ERC)	European Union	--
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2020-12-23
Changes: Structure summary
Version 1.2: 2020-12-30
Changes: Database references
Version 1.3: 2024-05-15
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7ARV | pdb_00007arv

TwistTower_native-twist

Literature

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.

Biological Assembly 1

Macromolecules

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