[English] 日本語
Yorodumi
- PDB-1br4: SMOOTH MUSCLE MYOSIN MOTOR DOMAIN-ESSENTIAL LIGHT CHAIN COMPLEX W... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1br4
TitleSMOOTH MUSCLE MYOSIN MOTOR DOMAIN-ESSENTIAL LIGHT CHAIN COMPLEX WITH MGADP.BEF3 BOUND AT THE ACTIVE SITE
Components(MYOSIN) x 2
KeywordsMUSCLE PROTEIN
Function / homologyMyosin S1 fragment, N-terminal / EF-hand domain / P-loop containing nucleoside triphosphate hydrolase / Myosin tail / EF-hand domain pair / Myosin IQ motif-containing domain superfamily / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin N-terminal SH3-like domain / EF-hand domain ...Myosin S1 fragment, N-terminal / EF-hand domain / P-loop containing nucleoside triphosphate hydrolase / Myosin tail / EF-hand domain pair / Myosin IQ motif-containing domain superfamily / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin N-terminal SH3-like domain / EF-hand domain / Myosin head (motor domain) / IQ motif profile. / Myosin tail / Myosin, N-terminal, SH3-like / EF-hand calcium-binding domain profile. / Myosin motor domain profile. / Myosin N-terminal SH3-like domain profile. / Smooth Muscle Contraction / RHO GTPases activate PAKs / Kinesin motor domain superfamily / myosin II filament / myosin light chain binding / myofibril assembly / muscle myosin complex / elastic fiber assembly / actomyosin structure organization / myosin II complex / myosin II binding / skeletal muscle myosin thick filament assembly / actin-dependent ATPase activity / myosin filament / microfilament motor activity / actomyosin / smooth muscle contraction / cardiac muscle fiber development / structural constituent of muscle / myofibril / myosin heavy chain binding / ADP binding / actin filament binding / actin binding / calmodulin binding / ATPase activity / calcium ion binding / protein heterodimerization activity / magnesium ion binding / ATP binding / cytosol / Myosin light polypeptide 6 / Myosin-11
Function and homology information
Specimen sourceGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.62 Å resolution
AuthorsDominguez, R. / Trybus, K.M. / Cohen, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a vertebrate smooth muscle myosin motor domain and its complex with the essential light chain: visualization of the pre-power stroke state.
Authors: Dominguez, R. / Freyzon, Y. / Trybus, K.M. / Cohen, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 27, 1998 / Release: Sep 9, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 9, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOSIN
B: MYOSIN
C: MYOSIN
D: MYOSIN
E: MYOSIN
F: MYOSIN
G: MYOSIN
H: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,35120
Polyers442,2818
Non-polymers2,07012
Water1448
1
A: MYOSIN
B: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polyers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5070
ΔGint (kcal/M)-38
Surface area (Å2)43730
MethodPISA
2
C: MYOSIN
D: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polyers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5060
ΔGint (kcal/M)-38
Surface area (Å2)43730
MethodPISA
3
E: MYOSIN
F: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polyers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5060
ΔGint (kcal/M)-38
Surface area (Å2)43630
MethodPISA
4
G: MYOSIN
H: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polyers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4920
ΔGint (kcal/M)-36
Surface area (Å2)43940
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)95.320, 144.660, 147.290
Angle α, β, γ (deg.)111.21, 106.10, 92.58
Int Tables number1
Space group name H-MP 1

-
Components

-
Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
MYOSIN / / MDE


Mass: 93697.180 Da / Num. of mol.: 4 / Details: MG, ADP, BEF(3)
Fragment: CHAINS A, C, E, G, MOTOR DOMAIN, CHAINS B, D, F, H, ESSENTIAL LIGHT
Source: (gene. exp.) Gallus gallus (chicken) / Genus: Gallus / Tissue: SMOOTH MUSCLE / Cell line: SF9 / Organ: GIZZARD / Genus (production host): Spodoptera / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587, EC: 3.6.1.32
#2: Protein/peptide
MYOSIN / / MDE


Mass: 16873.025 Da / Num. of mol.: 4 / Details: MG, ADP, BEF(3)
Fragment: CHAINS A, C, E, G, MOTOR DOMAIN, CHAINS B, D, F, H, ESSENTIAL LIGHT
Source: (gene. exp.) Gallus gallus (chicken) / Genus: Gallus / Tissue: SMOOTH MUSCLE / Cell line: SF9 / Organ: GIZZARD / Genus (production host): Spodoptera / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02607, EC: 3.6.1.32

-
Non-polymers , 4 types, 20 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4 / Density percent sol: 7 %
Crystal growTemp: 277 K / pH: 7.2
Details: 1.8M AMMONIUM SULFATE 100MM HEPES PH 7.2 2MM MGADP 2MM AL(NO3)3 8MM NAF PROTEIN CONCENTRATION: 10MG/ML TEMPERATURE: 4 DEGREES CENTIGRADE, temperature 277K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcUnitCommon nameSol IDChemical formula
110 mg/mlproteindrop
22 mMMgADPdrop
32 mMberyllium(SIGMA)drop
5Mammonium sulfatereservoir
6mMHEPESreservoir
4mMdropNaF

-
Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE A1 / Synchrotron site: CHESS / Beamline: A1 / Wavelength: 0.905
DetectorDetector: CCD / Collection date: Jul 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 / Relative weight: 1
ReflectionD resolution high: 3.62 / D resolution low: 2 / Number obs: 75979 / Rsym value: 0.111 / NetI over sigmaI: 13.7 / Redundancy: 6.3 % / Percent possible obs: 95.6
Reflection shellHighest resolution: 3.62 / Lowest resolution: 3.9 / MeanI over sigI obs: 6.9 / Rsym value: 0.331 / Redundancy: 4.1 % / Percent possible all: 94.2
Reflection
*PLUS
Number measured all: 478668 / Rmerge I obs: 0.111
Reflection shell
*PLUS
Percent possible obs: 94.2 / Rmerge I obs: 0.331

+
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SMOOTH MUSCLE MOTOR DOMAIN

R Free selection details: RANDOM / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 48.9
Least-squares processR factor R free: 0.352 / R factor R work: 0.277 / R factor obs: 0.277 / Highest resolution: 3.62 / Lowest resolution: 1 / Number reflection obs: 72931 / Percent reflection R free: 5 / Percent reflection obs: 95.7
Refine analyzeLuzzati coordinate error free: 0.7
Refine hist #LASTHighest resolution: 3.62 / Lowest resolution: 1
Number of atoms included #LASTProtein: 29824 / Nucleic acid: 0 / Ligand: 136 / Solvent: 8 / Total: 29968
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints ncsNcs model details: RESTRAINTS
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more