[English] 日本語
Yorodumi
- PDB-5wsu: Crystal structure of Myosin VIIa IQ5-SAH in complex with apo-CaM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wsu
TitleCrystal structure of Myosin VIIa IQ5-SAH in complex with apo-CaM
Components
  • Calmodulin
  • Unconventional myosin-VIIa
KeywordsMOTOR PROTEIN/CALCIUM BINDING PROTEIN / Molecular motor / Calcium signaling / Protein complex / Calmodulin / MOTOR PROTEIN-CALCIUM BINDING PROTEIN complex
Function / homology
Function and homology information


pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus ...pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / : / : / : / actin filament-based movement / : / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / sensory perception / stereocilium / establishment of protein localization to mitochondrial membrane / cell projection organization / type 3 metabotropic glutamate receptor binding / auditory receptor cell stereocilium organization / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / lysosome organization / inner ear morphogenesis / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / spectrin binding / microfilament motor activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / microvillus / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / inner ear development / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / cochlea development / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / photoreceptor outer segment / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / phagocytosis / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / eNOS activation
Similarity search - Function
Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. ...Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / IRS-type PTB domain / PTB domain (IRS-1 type) / IQ calmodulin-binding motif / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Unconventional myosin-VIIa
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, J. / Chen, Y. / Deng, Y. / Lu, Q. / Zhang, M.
CitationJournal: Structure / Year: 2017
Title: Ca(2+)-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single alpha Helix Lever Arm Extension
Authors: Li, J. / Chen, Y. / Deng, Y. / Unarta, I.C. / Lu, Q. / Huang, X. / Zhang, M.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Calmodulin
C: Unconventional myosin-VIIa
B: Calmodulin
D: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)59,9334
Polymers59,9334
Non-polymers00
Water00
1
A: Calmodulin
C: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)29,9672
Polymers29,9672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-24 kcal/mol
Surface area13520 Å2
MethodPISA
2
B: Calmodulin
D: Unconventional myosin-VIIa


Theoretical massNumber of molelcules
Total (without water)29,9672
Polymers29,9672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.930, 80.930, 175.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Calmodulin / CaM


Mass: 17019.646 Da / Num. of mol.: 2 / Fragment: UNP residues 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein Unconventional myosin-VIIa


Mass: 12946.976 Da / Num. of mol.: 2 / Fragment: UNP residues 834-935
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a, Myo7 / Production host: Escherichia coli (E. coli) / References: UniProt: P97479

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M sodium citrate tribasic (pH 5.6), 20%(v/v) isopropanol, 20%(w/v) PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 3→50 Å / Num. obs: 22489 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2 / Rsym value: 0.967 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IX7

2ix7


Resolution: 3→47.917 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.36
RfactorNum. reflection% reflection
Rfree0.2901 2002 8.93 %
Rwork0.2237 --
obs0.2308 22430 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→47.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 0 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063131
X-RAY DIFFRACTIONf_angle_d0.9374255
X-RAY DIFFRACTIONf_dihedral_angle_d16.9821869
X-RAY DIFFRACTIONf_chiral_restr0.048528
X-RAY DIFFRACTIONf_plane_restr0.007559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.07570.34121430.30621447X-RAY DIFFRACTION91
3.0757-3.15880.41711410.32971454X-RAY DIFFRACTION91
3.1588-3.25170.3581440.30621458X-RAY DIFFRACTION91
3.2517-3.35660.30521450.27541467X-RAY DIFFRACTION91
3.3566-3.47660.39821460.31141459X-RAY DIFFRACTION91
3.4766-3.61570.32781450.2841460X-RAY DIFFRACTION91
3.6157-3.78010.32551450.29861442X-RAY DIFFRACTION91
3.7801-3.97920.29231500.25521453X-RAY DIFFRACTION90
3.9792-4.22830.26241430.21411469X-RAY DIFFRACTION91
4.2283-4.55440.23921360.19531475X-RAY DIFFRACTION92
4.5544-5.01190.27491380.17191473X-RAY DIFFRACTION91
5.0119-5.73540.24791420.21111463X-RAY DIFFRACTION91
5.7354-7.21930.30771460.22551478X-RAY DIFFRACTION91
7.2193-40.46870.25491380.1641406X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.776-0.7515-0.85231.93841.00542.65340.1269-0.4466-0.3435-0.4158-0.23710.1442-0.84510.37830.06910.7705-0.14520.04740.2946-0.04210.546115.710172.61387.6071
24.6791.43993.30181.50011.62612.67580.36940.68471.0509-0.3561-0.446-0.5459-1.36750.4977-01.28870.08330.0310.67130.13370.679820.706181.8896-0.7621
30.32910.4285-0.50550.8071-0.11281.71250.16970.41180.2561-0.1996-0.01050.0912-1.143-0.6095-0.04520.78140.2534-0.06720.86530.03390.482311.707774.6189-10.3786
46.398-0.38390.49519.0294-1.33937.6212-0.12240.0773-0.85780.0190.2070.4208-0.49680.15-0.05930.5741-0.0947-0.20180.60410.12610.736717.206464.3567-14.8697
50.4535-0.8563-1.41262.94292.81694.40490.09410.7568-0.18250.1937-0.79680.6177-0.1852-0.68890.0760.43160.0568-0.04521.2089-0.25010.7925.872864.5617-15.5812
60.22790.13-0.20971.0936-1.97523.72540.1858-0.2247-0.16820.36690.34760.6339-0.3208-0.31610.06520.7687-0.054-0.00140.3090.10140.599317.661847.509322.7348
71.8411-0.2006-0.04061.04850.09491.64480.2025-0.5344-0.03830.0537-0.137-0.4947-0.38970.8882-0.10540.1729-0.20650.17491.10020.11990.722935.451157.6229-48.1306
82.0966-0.19920.73711.0237-0.63180.82460.11340.6550.68820.10190.64990.9149-0.27-0.9133-1.05680.98470.4326-0.63761.084-0.27991.710438.009844.5816-38.5461
90.75410.6767-1.12190.6308-1.10262.05760.19920.13080.010.5066-0.1391-0.2203-0.2150.07550.3581.41660.38620.03910.84810.5771.195133.069644.8278-21.1874
107.46276.4050.62957.66132.5493.95350.0597-0.42260.16290.5230.3611-0.26880.7185-0.1377-0.00830.57910.33370.1491.1680.28090.772927.00556.4243-19.6127
113.93241.5138-2.86636.5017-0.71434.3203-0.2551-0.4302-0.14851.1183-0.3807-1.34250.30370.76490.43671.0033-0.0418-0.17660.30660.28330.995232.375562.5977-26.0305
123.17773.5915-3.21074.3481-4.0563.87380.12590.28550.4148-0.09490.22770.21530.0866-0.34130.01220.62940.08780.12820.2190.30360.653522.953858.9559-28.5681
131.85861.2967-0.13623.789-3.0193.3618-0.05450.1336-0.56030.01860.2586-0.30520.87050.05950.09611.4177-0.21290.10490.3594-0.10261.174924.163345.9404-27.3145
140.5716-0.19210.88130.4776-0.29661.73980.22690.0805-0.1745-0.38040.06010.1289-0.13190.58850.10140.182-0.19350.04390.7563-0.02930.67087.635757.967-64.6292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 148 )
6X-RAY DIFFRACTION6chain 'C' and (resid 762 through 851 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 74 )
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 98 )
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 111 )
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 147 )
14X-RAY DIFFRACTION14chain 'D' and (resid 760 through 850 )

+
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