7ART | pdb_00007art

48 helix bundle DNA origami brick

PDB DOI: https://doi.org/10.2210/pdb7ART/pdb
NAKB: 7ART
EM Map EMD-11387: EMDB EMDataResource

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

Deposited: 2020-10-26 Released: 2020-11-11
Deposition Author(s): Feigl, E., Kube, M., Kohler, F., 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 10.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Currently 7ART does not have a validation slider image.

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 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: 5,263.66 kDa
Atom Count: 349,108
Modeled Residue Count: 17,084
Deposited Residue Count: 17,084
Unique nucleic acid chains: 212

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
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STAPLE STRAND	B [auth AB]	40	synthetic construct
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Entity ID: 3
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STAPLE STRAND	C [auth AC]	44	synthetic construct
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Entity ID: 4
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STAPLE STRAND	D [auth AD]	50	synthetic construct
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Entity ID: 5
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STAPLE STRAND	E [auth AE]	47	synthetic construct
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Entity ID: 6
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STAPLE STRAND	F [auth AF]	49	synthetic construct
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Entity ID: 7
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STAPLE STRAND	G [auth AG]	49	synthetic construct
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Entity ID: 8
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STAPLE STRAND	H [auth AH]	49	synthetic construct
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STAPLE STRAND	I [auth AI]	49	synthetic construct
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STAPLE STRAND	J [auth AJ]	42	synthetic construct
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Entity ID: 11
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STAPLE STRAND	K [auth AK]	54	synthetic construct
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STAPLE STRAND	L [auth AL]	38	synthetic construct
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STAPLE STRAND	M [auth AM]	44	synthetic construct
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STAPLE STRAND	N [auth AN]	35	synthetic construct
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STAPLE STRAND	O [auth AO]	40	synthetic construct
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STAPLE STRAND	R [auth AR]	49	synthetic construct
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STAPLE STRAND	S [auth AS]	42	synthetic construct
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Entity ID: 114
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STAPLE STRAND	JD [auth Bz]	49	synthetic construct
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STAPLE STRAND	KD [auth B0]	43	synthetic construct
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STAPLE STRAND	LD [auth B1]	49	synthetic construct
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STAPLE STRAND	MD [auth B2]	38	synthetic construct
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STAPLE STRAND	ND [auth B3]	44	synthetic construct
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STAPLE STRAND	OD [auth B4]	35	synthetic construct
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STAPLE STRAND	QD [auth B6]	49	synthetic construct
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STAPLE STRAND	SG [auth DO]	49	synthetic construct
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STAPLE STRAND	TG [auth DP]	35	synthetic construct
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STAPLE STRAND	UG [auth DQ]	49	synthetic construct
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STAPLE STRAND	VG [auth DR]	49	synthetic construct
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STAPLE STRAND	WG [auth DS]	49	synthetic construct
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STAPLE STRAND	XG [auth DT]	37	synthetic construct
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Entity ID: 207
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STAPLE STRAND	YG [auth DU]	42	synthetic construct
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STAPLE STRAND	ZG [auth DV]	50	synthetic construct
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Entity ID: 209
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STAPLE STRAND	AH [auth DW]	44	synthetic construct
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Entity ID: 210
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STAPLE STRAND	BH [auth DX]	40	synthetic construct
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Entity ID: 211
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STAPLE STRAND	CH [auth DY]	42	synthetic construct
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Entity ID: 212
Molecule	Chains	Length	Organism	Image
STAPLE STRAND	DH [auth DZ]	42	synthetic construct
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Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 10.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Currently 7ART does not have a validation slider image.

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Nagel-Yuksel, B.

Scheres, S.H.W.

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

Revision History (Full details and data files)

Version 1.0: 2020-11-11
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 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.