7ARY

Twist-Tower_twist-corrected-variant

PDB DOI: https://doi.org/10.2210/pdb7ARY/pdb
NAKB: 7ARY
EM Map EMD-11378: EMDB EMDataResource

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: 8.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Currently 7ARY does not have a validation slider image.

This is version 1.2 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-20020-7
Primary Citation of 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: 5,003.1 kDa
Atom Count: 331,913
Modelled Residue Count: 16,230
Deposited Residue Count: 16,230
Unique nucleic acid chains: 192

Macromolecules

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
SCAFFOLD STRAND	A [auth AA]	8,064	synthetic construct
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Entity ID: 2
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	B [auth AB]	47	synthetic construct
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Entity ID: 3
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	C [auth AC]	53	synthetic construct
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Entity ID: 4
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	D [auth AD]	48	synthetic construct
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Entity ID: 5
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	E [auth AE]	48	synthetic construct
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Entity ID: 6
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	F [auth AF]	55	synthetic construct
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Entity ID: 7
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	G [auth AG]	48	synthetic construct
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Entity ID: 8
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	H [auth AH]	31	synthetic construct
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Entity ID: 9
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	I [auth AI]	28	synthetic construct
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Entity ID: 10
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STAPLE STRAND	J [auth AJ]	48	synthetic construct
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Entity ID: 11
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STAPLE STRAND	K [auth AK]	32	synthetic construct
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Entity ID: 12
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	L [auth AL]	52	synthetic construct
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Entity ID: 13
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	M [auth AM]	38	synthetic construct
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STAPLE STRAND	N [auth AN]	46	synthetic construct
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STAPLE STRAND	O [auth AO]	46	synthetic construct
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STAPLE STRAND	P [auth AP]	48	synthetic construct
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STAPLE STRAND	Q [auth AQ]	48	synthetic construct
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STAPLE STRAND	R [auth AR]	46	synthetic construct
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STAPLE STRAND	S [auth AS]	50	synthetic construct
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STAPLE STRAND	T [auth AT]	47	synthetic construct
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STAPLE STRAND	U [auth AU]	40	synthetic construct
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STAPLE STRAND	V [auth AV]	45	synthetic construct
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STAPLE STRAND	W [auth AW]	48	synthetic construct
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STAPLE STRAND	X [auth AX]	37	synthetic construct
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STAPLE STRAND	Z [auth AZ]	40	synthetic construct
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STAPLE STRAND	AA [auth Aa]	53	synthetic construct
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Entity ID: 28
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STAPLE STRAND	BA [auth Ab]	39	synthetic construct
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Entity ID: 29
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STAPLE STRAND	CA [auth Ac]	31	synthetic construct
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Entity ID: 30
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STAPLE STRAND	DA [auth Ad]	45	synthetic construct
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STAPLE STRAND	EA [auth Ae]	52	synthetic construct
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STAPLE STRAND	FA [auth Af]	46	synthetic construct
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STAPLE STRAND	GA [auth Ag]	30	synthetic construct
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Entity ID: 34
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Entity ID: 35
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STAPLE STRAND	IA [auth Ai]	48	synthetic construct
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Entity ID: 37
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STAPLE STRAND	KA [auth Ak]	38	synthetic construct
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Entity ID: 38
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STAPLE STRAND	LA [auth Al]	56	synthetic construct
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Entity ID: 39
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STAPLE STRAND	MA [auth Am]	38	synthetic construct
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Entity ID: 40
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STAPLE STRAND	NA [auth An]	45	synthetic construct
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Entity ID: 41
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STAPLE STRAND	OA [auth Ao]	46	synthetic construct
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Entity ID: 42
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STAPLE STRAND	PA [auth Ap]	48	synthetic construct
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Entity ID: 43
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STAPLE STRAND	QA [auth Aq]	32	synthetic construct
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Entity ID: 44
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STAPLE STRAND	RA [auth Ar]	48	synthetic construct
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STAPLE STRAND	SA [auth As]	48	synthetic construct
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STAPLE STRAND	TA [auth At]	54	synthetic construct
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STAPLE STRAND	UA [auth Au]	46	synthetic construct
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STAPLE STRAND	VA [auth Av]	48	synthetic construct
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Entity ID: 51
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STAPLE STRAND	YA [auth Ay]	31	synthetic construct
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Entity ID: 52
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STAPLE STRAND	ZA [auth Az]	30	synthetic construct
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Entity ID: 53
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STAPLE STRAND	AB [auth A0]	32	synthetic construct
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STAPLE STRAND	BB [auth A1]	48	synthetic construct
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STAPLE STRAND	DB [auth A3]	30	synthetic construct
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STAPLE STRAND	EB [auth A4]	45	synthetic construct
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Entity ID: 58
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STAPLE STRAND	FB [auth A5]	45	synthetic construct
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Entity ID: 59
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STAPLE STRAND	GB [auth A6]	48	synthetic construct
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Entity ID: 60
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STAPLE STRAND	HB [auth A7]	48	synthetic construct
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STAPLE STRAND	IB [auth A8]	60	synthetic construct
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Entity ID: 62
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STAPLE STRAND	JB [auth A9]	38	synthetic construct
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STAPLE STRAND	LB [auth BB]	31	synthetic construct
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Entity ID: 66
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Entity ID: 107
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	CD [auth Bs]	30	synthetic construct
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STAPLE STRAND	DD [auth Bt]	45	synthetic construct
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STAPLE STRAND	ED [auth Bu]	49	synthetic construct
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STAPLE STRAND	FD [auth Bv]	40	synthetic construct
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STAPLE STRAND	GD [auth Bw]	37	synthetic construct
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STAPLE STRAND	HD [auth Bx]	52	synthetic construct
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STAPLE STRAND	ID [auth By]	30	synthetic construct
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STAPLE STRAND	JD [auth Bz]	40	synthetic construct
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STAPLE STRAND	KD [auth B0]	30	synthetic construct
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STAPLE STRAND	LD [auth B1]	52	synthetic construct
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STAPLE STRAND	ND [auth B3]	56	synthetic construct
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STAPLE STRAND	OD [auth B4]	48	synthetic construct
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STAPLE STRAND	QD [auth B6]	45	synthetic construct
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STAPLE STRAND	RD [auth B7]	37	synthetic construct
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STAPLE STRAND	XD [auth CD]	59	synthetic construct
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STAPLE STRAND	KE [auth CQ]	48	synthetic construct
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STAPLE STRAND	RE [auth CX]	48	synthetic construct
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STAPLE STRAND	UE [auth Ca]	39	synthetic construct
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STAPLE STRAND	DF [auth Cj]	54	synthetic construct
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STAPLE STRAND	JF [auth Cp]	37	synthetic construct
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STAPLE STRAND	NF [auth Ct]	38	synthetic construct
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STAPLE STRAND	QF [auth Cw]	31	synthetic construct
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STAPLE STRAND	UF [auth C0]	60	synthetic construct
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STAPLE STRAND	XF [auth C3]	37	synthetic construct
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STAPLE STRAND	YF [auth C4]	57	synthetic construct
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STAPLE STRAND	ZF [auth C5]	44	synthetic construct
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Entity ID: 183
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STAPLE STRAND	AG [auth C6]	47	synthetic construct
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Entity ID: 184
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STAPLE STRAND	BG [auth C7]	47	synthetic construct
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Entity ID: 185
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STAPLE STRAND	CG [auth C8]	38	synthetic construct
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Entity ID: 186
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	DG [auth C9]	37	synthetic construct
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Entity ID: 187
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STAPLE STRAND	EG [auth DA]	60	synthetic construct
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Entity ID: 188
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STAPLE STRAND	FG [auth DB]	43	synthetic construct
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Entity ID: 189
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STAPLE STRAND	GG [auth DC]	46	synthetic construct
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Entity ID: 190
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STAPLE STRAND	HG [auth DD]	38	synthetic construct
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Entity ID: 191
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STAPLE STRAND	IG [auth DE]	46	synthetic construct
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Entity ID: 192
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	JG [auth DF]	31	synthetic construct
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Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3

Structure Validation

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Currently 7ARY does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Nagel-Yuksel, B.

Scheres, S.H.W.

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.