1ATN

Atomic structure of the actin:DNASE I complex

PDB DOI: https://doi.org/10.2210/pdb1ATN/pdb

Classification: ENDODEOXYRIBONUCLEASE
Organism(s): Oryctolagus cuniculus, Bos taurus
Mutation(s): No

Deposited: 1991-03-08 Released: 1992-07-15
Deposition Author(s): Kabsch, W., Mannherz, H.G., Suck, D., Pai, E., Holmes, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Atomic structure of the actin:DNase I complex.

Kabsch, W., Mannherz, H.G., Suck, D., Pai, E.F., Holmes, K.C.

(1990) Nature 347: 37-44

PubMed: 2395459 Search on PubMed
DOI: https://doi.org/10.1038/347037a0
Primary Citation of Related Structures:
1ATN

PubMed Abstract:
The atomic models of the complex between rabbit skeletal muscle actin and bovine pancreatic deoxyribonuclease I both in the ATP and ADP forms have been determined by X-ray analysis at an effective resolution of 2.8 A and 3A, respectively. The two structures are very similar. The actin molecule consists of two domains which can be further subdivided into two subdomains. ADP or ATP is located in the cleft between the domains with a calcium ion bound to the beta- or beta- and gamma-phosphates, respectively. The motif of a five-stranded beta sheet consisting of a beta meander and a right handed beta alpha beta unit appears in each domain suggesting that gene duplication might have occurred. These sheets have the same topology as that found in hexokinase.

Organizational Affiliation

Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Heidelberg, FRG.

Macromolecule Content

Total Structure Weight: 71.82 kDa
Atom Count: 5,019
Modelled Residue Count: 631
Deposited Residue Count: 633
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN	A	373	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYRIBONUCLEASE I	B [auth D]	260	Bos taurus	Mutation(s): 0 EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus) Explore P00639 Go to UniProtKB: P00639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00639
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	3		N-Glycosylation	Interactions Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain H [auth D] SDF format, chain D [auth A] SDF format, chain G [auth D] MOL2 format, chain F [auth D] MOL2 format, chain H [auth D] MOL2 format, chain D [auth A] MOL2 format, chain G [auth D] mmCIF format, chain F [auth D] mmCIF format, chain H [auth D] mmCIF format, chain D [auth A] mmCIF format, chain G [auth D]	D [auth A], F [auth D], G [auth D], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Work: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.9	α = 90
b = 56.3	β = 90
c = 109.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1992-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1992-07-15
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-11-29
Changes: Derived calculations, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary