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- PDB-1atn: Atomic structure of the actin:DNASE I complex -

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Basic information

Entry
Database: PDB / ID: 1atn
TitleAtomic structure of the actin:DNASE I complex
Components
  • ACTIN
  • DEOXYRIBONUCLEASE I
KeywordsENDODEOXYRIBONUCLEASE
Function / homology
Function and homology information


Striated Muscle Contraction / regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / zymogen granule / deoxyribonuclease I / dynactin complex / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / cytoskeletal motor activator activity ...Striated Muscle Contraction / regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / zymogen granule / deoxyribonuclease I / dynactin complex / deoxyribonuclease I activity / neutrophil activation involved in immune response / DNA catabolic process / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / nuclear envelope / actin binding / cell body / hydrolase activity / protein domain specific binding / apoptotic process / calcium ion binding / positive regulation of gene expression / magnesium ion binding / DNA binding / extracellular region / ATP binding / nucleus / identical protein binding / cytoplasm
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase ...Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 4-Layer Sandwich / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Deoxyribonuclease-1 / Actin, alpha skeletal muscle / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKabsch, W. / Mannherz, H.G. / Suck, D. / Pai, E. / Holmes, K.C.
Citation
Journal: Nature / Year: 1990
Title: Atomic structure of the actin:DNase I complex.
Authors: Kabsch, W. / Mannherz, H.G. / Suck, D. / Pai, E.F. / Holmes, K.C.
#1: Journal: Annu.Rev.Biophys.Biophys.Chem. / Year: 1992
Title: Structure and Function of Actin
Authors: Kabsch, W. / Vandekerckhove, J.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1991
Title: Muscle Proteins: Actin
Authors: Holmes, K.C. / Kabsch, W.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Similarity of the Three-Dimensional Structures of Actin and the ATPase Fragment of a 70-kDa Heat Shock Cognate Protein
Authors: Flaherty, K.M. / Mckay, D.B. / Kabsch, W. / Holmes, K.C.
#4: Journal: Nature / Year: 1990
Title: Atomic Model of the Actin Filament
Authors: Holmes, K.C. / Popp, D. / Gebhard, W. / Kabsch, W.
#5: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic Refinement and Structure of DNase I at 2 Angstroms Resolution
Authors: Oefner, C. / Suck, D.
#6: Journal: Embo J. / Year: 1985
Title: Three-Dimensional Structure of the Complex of Actin and DNase I at 4.5 Angstroms Resolution
Authors: Kabsch, W. / Mannherz, H.G. / Suck, D.
#7: Journal: Embo J. / Year: 1984
Title: Three-Dimensional Structure of Bovine Pancreatic DNase I at 2.5 Angstroms Resolution
Authors: Suck, D. / Oefner, C. / Kabsch, W.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Three-Dimensional Structure of the Complex of Skeletal Muscle Actin and Bovine Pancreatic DNase I at 6-Angstroms Resolution
Authors: Suck, D. / Kabsch, W. / Mannherz, H.G.
History
DepositionMar 8, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700SHEET SHEETS A4A AND A4B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO ...SHEET SHEETS A4A AND A4B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS SPLIT INTO TWO DISTINCT AMINO ACID RUNS. THE BULGE OF 5 AMINO ACIDS INCLUDES HELIX 7. SHEET D1B IS AN EXTENSION OF SHEET D1A. STRANDS 1 TO 4 OF D1B ARE AN EXTENSION OF STRANDS 2 TO 5 OF D1A. SHEETS D2A AND D2B ARE IDENTICAL EXCEPT FOR THE FIRST STRAND. THIS STRAND IS INTERRUPTED BY ONE BULGE RESIDUE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACTIN
D: DEOXYRIBONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8248
Polymers70,5702
Non-polymers1,2546
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-52 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.900, 56.300, 109.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE HIS A 73 IS A METHYLATED HISTIDINE.

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Components

#1: Protein ACTIN /


Mass: 41522.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: PANCREAS / Tissue: MUSCLESkeletal muscle / References: UniProt: P02568, UniProt: P68135*PLUS
#2: Protein DEOXYRIBONUCLEASE I /


Mass: 29047.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / Tissue: MUSCLESkeletal muscle / References: UniProt: P00639
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Nonpolymer detailsTHERE IS A CARBOHYDRATE MOIETY CONSISTING OF TWO N-ACETYLGLUCOSAMINE AND 5 MANNOSE RESIDUES WHICH ...THERE IS A CARBOHYDRATE MOIETY CONSISTING OF TWO N-ACETYLGLUCOSAMINE AND 5 MANNOSE RESIDUES WHICH IS LINKED TO THE SIDE CHAIN AMIDE GROUP (ND2) OF ASN D 18 OF DNASE I THROUGH A BETA-1-N-GLYCOSIDIC BOND. THE FOUR MANNOSE RESIDUES FOLLOWING THE BRANCH AFTER MANNOSE 3 ARE NOT VISIBLE IN THE MAP AND HAVE BEEN OMITTED. THE RESIDUES DESIGNATED "CA" ARE DIVALENT METALS, PROBABLY CALCIUM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
250 mMimidazole 11
30.1 mM11CaCl2
41 mM11NaN3
52 mMMgATP1411
69 %PEG600012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. all: 32996 / Num. obs: 31362 / % possible obs: 81 % / Observed criterion σ(I): 1 / Num. measured all: 103367 / Rmerge(I) obs: 0.107

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→10 Å / Rfactor Rwork: 0.21 / σ(I): 1
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4945 0 74 0 5019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.2
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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