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- PDB-1o1b: MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF... -

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Entry
Database: PDB / ID: 1o1b
TitleMOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE
Components
  • SKELETAL MUSCLE ACTIN
  • SKELETAL MUSCLE MYOSIN II
  • SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN
  • SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN
KeywordsCONTRACTILE PROTEIN / ACTIN-MYOSIN COMPLEX IN SITU IN MUSCLE
Function / homology
Function and homology information


contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin II complex / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / myofibril / tropomyosin binding / myosin heavy chain binding ...contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin II complex / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / myofibril / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / skeletal muscle tissue development / muscle contraction / 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 / actin filament binding / lamellipodium / cell body / calmodulin binding / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / EF-hand domain pair / : / Myosin, N-terminal, SH3-like ...: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / EF-hand domain pair / : / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 3, skeletal muscle isoform / Myosin regulatory light chain 11 / Myosin heavy chain, skeletal muscle, adult / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / electron tomography / negative staining / Resolution: 70 Å
AuthorsChen, L.F. / Winkler, H. / Reedy, M.K. / Reedy, M.C. / Taylor, K.A.
Citation
Journal: J Struct Biol / Year: 2002
Title: Molecular modeling of averaged rigor crossbridges from tomograms of insect flight muscle.
Authors: Li Fan Chen / Hanspeter Winkler / Michael K Reedy / Mary C Reedy / Kenneth A Taylor /
Abstract: Electron tomography, correspondence analysis, molecular model building, and real-space refinement provide detailed 3-D structures for in situ myosin crossbridges in the nucleotide-free state (rigor), ...Electron tomography, correspondence analysis, molecular model building, and real-space refinement provide detailed 3-D structures for in situ myosin crossbridges in the nucleotide-free state (rigor), thought to represent the end of the power stroke. Unaveraged tomograms from a 25-nm longitudinal section of insect flight muscle preserved native structural variation. Recurring crossbridge motifs that repeat every 38.7 nm along the actin filament were extracted from the tomogram and classified by correspondence analysis into 25 class averages, which improved the signal to noise ratio. Models based on the atomic structures of actin and of myosin subfragment 1 were rebuilt to fit 11 class averages. A real-space refinement procedure was applied to quantitatively fit the reconstructions and to minimize steric clashes between domains introduced during the fitting. These combined procedures show that no single myosin head structure can fit all the in situ crossbridges. The validity of the approach is supported by agreement of these atomic models with fluorescent probe data from vertebrate muscle as well as with data from regulatory light chain crosslinking between heads of smooth muscle heavy meromyosin when bound to actin.
#1: Journal: J.Struct.Biol. / Year: 2001
Title: Real Space Refinement of Acto-Myosin Structures from Sectioned Muscle.
Authors: Chen, L.F. / Blanc, E. / Chapman, M.S. / Taylor, K.A.
#2: Journal: Ultramicroscopy / Year: 1999
Title: Multivariate Statistical Analysis of Three-Dimensional Cross-Bridge Motifs in Insect Flight Muscle
Authors: Winkler, H. / Taylor, K.A.
#3: Journal: J.Struct.Biol. / Year: 1997
Title: The Use of Electron Tomography for Structural Analysis of Disordered Protein Arrays.
Authors: Taylor, K.A. / Tang, J. / Cheng, Y. / Winkler, H.
History
DepositionNov 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_validate_symm_contact / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Remark 999SEQUENCE Since the models used to fit the data are not from the same source, the DBREF and the ...SEQUENCE Since the models used to fit the data are not from the same source, the DBREF and the SEQADV remarks were suppressed.

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Structure visualization

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Assembly

Deposited unit
A: SKELETAL MUSCLE MYOSIN II
B: SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN
C: SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN
D: SKELETAL MUSCLE MYOSIN II
E: SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN
F: SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN
G: SKELETAL MUSCLE MYOSIN II
H: SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN
I: SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN
J: SKELETAL MUSCLE MYOSIN II
K: SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN
L: SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN
0: SKELETAL MUSCLE ACTIN
1: SKELETAL MUSCLE ACTIN
2: SKELETAL MUSCLE ACTIN
3: SKELETAL MUSCLE ACTIN
4: SKELETAL MUSCLE ACTIN
5: SKELETAL MUSCLE ACTIN
7: SKELETAL MUSCLE ACTIN
8: SKELETAL MUSCLE ACTIN
9: SKELETAL MUSCLE ACTIN
V: SKELETAL MUSCLE ACTIN
W: SKELETAL MUSCLE ACTIN
X: SKELETAL MUSCLE ACTIN
Y: SKELETAL MUSCLE ACTIN
Z: SKELETAL MUSCLE ACTIN


Theoretical massNumber of molelcules
Total (without water)1,101,08626
Polymers1,101,08626
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
SKELETAL MUSCLE MYOSIN II


Mass: 96625.484 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ORGANISM FROM WHICH THE MYOSIN FOR THE CRYSTAL STRUCTURE THAT PROVIDED 2MYS WAS OBTAINED
Source: (natural) Gallus gallus (chicken) / References: UniProt: P13538
#2: Protein
SKELETAL MUSCLE MYOSIN II REGULATORY LIGHT CHAIN


Mass: 16063.036 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ORGANISM FROM WHICH THE MYOSIN FOR THE CRYSTAL STRUCTURE THAT PROVIDED 2MYS WAS OBTAINED
Source: (natural) Gallus gallus (chicken) / References: UniProt: P02609
#3: Protein
SKELETAL MUSCLE MYOSIN II ESSENTIAL LIGHT CHAIN


Mass: 16063.926 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ORGANISM FROM WHICH THE MYOSIN FOR THE CRYSTAL STRUCTURE THAT PROVIDED 2MYS WAS OBTAINED
Source: (natural) Gallus gallus (chicken) / References: UniProt: P02605
#4: Protein
SKELETAL MUSCLE ACTIN


Mass: 41862.613 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Details: ORGANISM FROM WHICH THE ACTIN THAT PROVIDED THE CRYSTAL STRUCTURE FOR 1ATN WAS OBTAINED
Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: INSECT FLIGHT MUSCLE OF THE LARGE WATER BUG LETHOCERUS MAXIMUS
Type: TISSUE
Details: DORSAL LONGITUDINAL FLIGHT MUSCLES OF THE LARGE WATERBUG, LETHOCERUS MAXIMUS WERE GLYCERINATED IN THE DISSECTED THORAX AND STORED AT -20 DEGREES C. FIXATION INVOLVED SEQUENTIAL TANNIC ACID- ...Details: DORSAL LONGITUDINAL FLIGHT MUSCLES OF THE LARGE WATERBUG, LETHOCERUS MAXIMUS WERE GLYCERINATED IN THE DISSECTED THORAX AND STORED AT -20 DEGREES C. FIXATION INVOLVED SEQUENTIAL TANNIC ACID-GLUTARALDEHYDE (0.2% AND 2%), COLD 1% OSO4 AT PH 6.0, 1% URANYL ACETATE BLOCK STAINING AND ARALDITE 506 EMGEDDING. THIN SECTIONS WERE STAINED WITH A SEQUENCE OF PERMANGANATE AND LEAD. SECTION WERE ~25 NM THICK. MODELS ARE BUILT TO FIT THE THIN, ACTIN CONTAINING FILAMENTS LABELED WITH ENDOGENOUS MYOSIN IN THE RIGOR STATE.
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Osmium tetroxide, Uranyl Acetate
VitrificationDetails: NO VITRIFICATION. SAMPLES WERE VIEWED AT ROOM TEMPERATURE.

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM400
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 17000 X
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 36
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1RSRefmodel fitting
2Custom3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: DUAL AXIS TILT SERIES ELECTRON TOMOGRAPHY / Resolution: 70 Å / Nominal pixel size: 15.5 Å
Magnification calibration: INDICATED INSTRUMENT MAGNIFICATION
Details: 3-D MOTIFS WERE IDENTIFIED IN THE TOMOGRAM BY FIRST PRODUCING A CROSS CORRELATION MAP FROM WHICH PEAK COORDINATES WERE DETERMINED FROM THEIR CENTER OF GRAVITY. WE DEFINE A 3-D MOTIF AS ONE, ...Details: 3-D MOTIFS WERE IDENTIFIED IN THE TOMOGRAM BY FIRST PRODUCING A CROSS CORRELATION MAP FROM WHICH PEAK COORDINATES WERE DETERMINED FROM THEIR CENTER OF GRAVITY. WE DEFINE A 3-D MOTIF AS ONE, ENTIRE 38.7 NM CROSSBRIDGE REPEAT ALONG ACTIN. THESE MOTIFS USUALLY CONTAIN AT LEAST FOUR MYOSIN HEADS IN TWO PAIRED CROSSBRIDGES (SINGLE CHEVRONS) AND SOMETIMES CONTAIN AS MANY AS SIX MYOSIN HEADS IN FOUR PAIRED CROSSBRIDGES (DOUBLE CHEVRONS). THE REFERENCE FOR THE ANALYSIS WAS SELECTED TO BE CENTERED BETWEEN SUCCESSIVE TROPONIN DENSITIES WHICH COULD BE IDENTIFIED FROM THE IN-PLANE PROJECTION. THE INDIVIDUAL CROSSBRIDGE MOTIFS WERE THEN SUBJECTED TO MULTIVARIATE STATISTICAL ANALYSIS TO IDENTIFY CLUSTERS OF MOTIFS SHOWING SIMILAR CROSSBRIDGE STRUCTURE. THESE CLUSTERS FORMED THE CLASS AVERAGES. THE CHOICE OF STRUCTURE TO BE CLASSIFIED WAS DECIDED BY THE RESOLUTION AND THE LATER PROCESS OF MODEL BUILDING. AVERAGING WAS DONE ACCORDING TO THE HEIRARCHICAL ASCENDENT METHOD. THE RESOLUTION IN EACH OF THE CLASS AVERAGES WAS 7 NM BY THE SPECTRAL SIGNAL TO NOISE RATIO.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: BEST CORRELATION COEFFICIENT AND FEWEST POOR CONTACTS
Details: METHOD--INITIAL MODELS WERE FIT BY HAND USING O. THE FIT WAS THEN REFINED USING REAL SPACE REFINEMENT. REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12MYS

2mys

12MYS1PDBexperimental model
21ATN

1atn

11ATN2PDBexperimental model
RefinementHighest resolution: 70 Å
Refinement stepCycle: LAST / Highest resolution: 70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76872 0 0 0 76872

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