[English] 日本語
Yorodumi
- PDB-5wsv: Crystal structure of Myosin VIIa IQ5 in complex with Ca2+-CaM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wsv
TitleCrystal structure of Myosin VIIa IQ5 in complex with Ca2+-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 cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / sensory perception / cell projection organization / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / stereocilium / auditory receptor cell stereocilium organization / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / inner ear morphogenesis / lysosome organization / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / spectrin binding / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / microfilament motor activity / cochlea development / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / inner ear development / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / microvillus / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / photoreceptor outer segment / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / phagocytosis / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling
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 / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 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: 2.33 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin
B: Unconventional myosin-VIIa
C: Calmodulin
D: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82715
Polymers45,2194
Non-polymers60911
Water21612
1
A: Calmodulin
B: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7706
Polymers22,6092
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-48 kcal/mol
Surface area8290 Å2
MethodPISA
2
C: Calmodulin
D: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0589
Polymers22,6092
Non-polymers4497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-120 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.683, 89.755, 45.724
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Calmodulin / CaM


Mass: 16950.584 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147
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/peptide Unconventional myosin-VIIa


Mass: 5658.692 Da / Num. of mol.: 2 / Fragment: UNP residues 828-870
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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.69 Å3/Da / Density % sol: 27.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris (pH 6.5), 25%(w/v) PEG 3,500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 12459 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.36 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G43

3g43


Resolution: 2.33→44.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 25.713 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.643 / ESU R Free: 0.289
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 598 4.8 %RANDOM
Rwork0.2281 ---
obs0.2298 11840 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.27 Å2 / Biso mean: 45.433 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0.21 Å2
2--1.04 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.33→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 23 12 2500
Biso mean--63.41 36.69 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192517
X-RAY DIFFRACTIONr_bond_other_d0.0020.022216
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9433419
X-RAY DIFFRACTIONr_angle_other_deg0.98235040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9925339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09325.714112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.768159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
X-RAY DIFFRACTIONr_mcbond_it1.5153.3321362
X-RAY DIFFRACTIONr_mcbond_other1.5153.331361
X-RAY DIFFRACTIONr_mcangle_it2.5064.9871696
LS refinement shellResolution: 2.329→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 29 -
Rwork0.315 769 -
all-798 -
obs--85.53 %
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)
10.73830.15010.23140.3693-0.45861.2183-0.021-0.08610.1091-0.08040.0691-0.09560.125-0.1539-0.04810.0405-0.01790.00920.0324-0.04460.227441.3881-75.168350.0792
21.23110.07560.90060.09070.16730.80940.0967-0.14450.10560.0271-0.1227-0.00690.1167-0.23330.0260.0695-0.01830.00150.1471-0.01430.18237.1482-73.018652.5876
30.6681-0.52140.58280.77510.40052.51310.06310.12710.097-0.0212-0.1598-0.05270.1059-0.02220.09670.0582-0.02050.02430.05240.02610.142127.839-76.702428.0984
41.2804-1.27670.9992.9689-1.1730.9590.2314-0.1676-0.0527-0.2284-0.1909-0.0270.0548-0.1365-0.04040.14040.0055-0.01610.11320.00660.103624.5869-79.180328.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 144
2X-RAY DIFFRACTION2B826 - 854
3X-RAY DIFFRACTION3C5 - 146
4X-RAY DIFFRACTION4D828 - 856

+
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