[English] 日本語
Yorodumi
- PDB-5xgg: Crystal Structure C-terminal SH3 domain of Myosin IB from Entamoe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xgg
TitleCrystal Structure C-terminal SH3 domain of Myosin IB from Entamoeba histolytica
ComponentsUnconventional myosin IB
KeywordsCONTRACTILE PROTEIN / SH3 / MyosinI / Entamoeba histolytica / EhMySH3
Function / homology
Function and homology information


phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium ...phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium / myosin light chain binding / actin-myosin filament sliding / actomyosin / filopodium assembly / vesicle transport along actin filament / microfilament motor activity / endosomal transport / exocytosis / phagocytosis / filopodium / actin filament organization / cell motility / phospholipid binding / endocytosis / phagocytic vesicle membrane / actin filament binding / cell-cell junction / actin cytoskeleton / vesicle / early endosome / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Unconventional myosin IB
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGautam, G. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
SERB India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition
Authors: Gautam, G. / Rehman, S.A.A. / Pandey, P. / Gourinath, S.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unconventional myosin IB
B: Unconventional myosin IB
C: Unconventional myosin IB
D: Unconventional myosin IB
E: Unconventional myosin IB
F: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3308
Polymers46,1376
Non-polymers1922
Water11,638646
1
A: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
2
B: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7862
Polymers7,6901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-14 kcal/mol
Surface area4740 Å2
MethodPISA
3
C: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
4
D: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7862
Polymers7,6901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area4720 Å2
MethodPISA
5
E: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4770 Å2
MethodPISA
6
F: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 77.670, 61.830
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Unconventional myosin IB / Unconventional myosin ib


Mass: 7689.563 Da / Num. of mol.: 6 / Fragment: SH3 domain, UNP residues 995-1049
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: CL6EHI_110810, EHI_110810 / Plasmid: pET-21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4LUC7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.2M ammonium sulphate, 5% v/v isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→77.67 Å / Num. obs: 101866 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.027 / Rsym value: 0.11 / Χ2: 1.94 / Net I/av σ(I): 25.2 / Net I/σ(I): 4.17
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.17 / CC1/2: 0.96 / Rpim(I) all: 0.185 / Rsym value: 0.43 / Χ2: 0.82 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4iim

4iim


Resolution: 1.72→58.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.099 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21878 2512 5.1 %RANDOM
Rwork0.18458 ---
obs0.18627 47114 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.04 Å2
2---0.18 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.72→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 10 649 3720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193156
X-RAY DIFFRACTIONr_bond_other_d0.0020.022888
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9364293
X-RAY DIFFRACTIONr_angle_other_deg1.0436679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4225374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86226.346156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74615521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5341.2011514
X-RAY DIFFRACTIONr_mcbond_other1.5261.21513
X-RAY DIFFRACTIONr_mcangle_it2.2731.791882
X-RAY DIFFRACTIONr_mcangle_other2.2731.7911883
X-RAY DIFFRACTIONr_scbond_it2.8841.5521642
X-RAY DIFFRACTIONr_scbond_other2.881.5491635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3542.1822399
X-RAY DIFFRACTIONr_long_range_B_refined7.76213.364226
X-RAY DIFFRACTIONr_long_range_B_other6.89311.3533751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 170 -
Rwork0.212 3511 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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