[English] 日本語
Yorodumi
- PDB-6ku0: Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ku0
TitleCrystal structure of MyoVa-GTD in complex with MICAL1-GTBM
Components
  • Peptide from [F-actin]-monooxygenase MICAL1
  • Unconventional myosin-Va
KeywordsPROTEIN BINDING / Complex / Cargo binding
Function / homology
Function and homology information


actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / hippocampal mossy fiber expansion / endoplasmic reticulum localization / melanosome localization / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) ...actomyosin, myosin complex part / establishment of endoplasmic reticulum localization to postsynapse / axo-dendritic protein transport / positive regulation of cellular response to insulin stimulus / hippocampal mossy fiber expansion / endoplasmic reticulum localization / melanosome localization / NADPH oxidase H202-forming activity / F-actin monooxygenase / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / locomotion involved in locomotory behavior / reactive gliosis / melanin metabolic process / regulation of regulated secretory pathway / unconventional myosin complex / post-Golgi vesicle-mediated transport / insulin-responsive compartment / negative regulation of dopamine secretion / NAD(P)H oxidase H2O2-forming activity / developmental pigmentation / regulation of postsynaptic cytosolic calcium ion concentration / melanosome transport / actin filament-based movement / melanin biosynthetic process / secretory granule localization / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / Regulation of actin dynamics for phagocytic cup formation / filopodium tip / hair follicle maturation / melanocyte differentiation / postsynaptic actin cytoskeleton / actomyosin / regulation of exocytosis / negative regulation of synaptic transmission, glutamatergic / actin filament depolymerization / vesicle transport along actin filament / ATP-dependent protein binding / positive regulation of vascular associated smooth muscle cell migration / long-chain fatty acid biosynthetic process / syntaxin-1 binding / insulin secretion / myosin complex / intermediate filament / odontogenesis / pigmentation / microfilament motor activity / dopamine metabolic process / intercellular bridge / exocytosis / smooth endoplasmic reticulum / actin filament bundle assembly / cytoskeletal motor activity / photoreceptor outer segment / cytoskeleton organization / vesicle-mediated transport / ruffle / myelination / visual perception / FAD binding / SNARE binding / negative regulation of protein phosphorylation / secretory granule / actin filament organization / actin filament / protein localization to plasma membrane / monooxygenase activity / synapse organization / positive regulation of protein localization to plasma membrane / macroautophagy / Schaffer collateral - CA1 synapse / recycling endosome / small GTPase binding / SH3 domain binding / cellular response to insulin stimulus / calcium-dependent protein binding / disordered domain specific binding / melanosome / actin filament binding / synaptic vesicle / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / chemical synaptic transmission / postsynapse / protein-containing complex assembly / vesicle / calmodulin binding / endosome membrane / ribonucleoprotein complex / axon / dendrite / neuronal cell body / glutamatergic synapse / calcium ion binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus
Similarity search - Function
DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL ...DUF3585 / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / IQ calmodulin-binding motif / FAD-binding domain / FAD binding domain / Calponin homology domain / Calponin homology (CH) domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / FAD/NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
[F-actin]-monooxygenase MICAL1 / Unconventional myosin-Va
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNiu, F. / Wei, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31800643 China
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: Sci Adv / Year: 2020
Title: F-actin disassembly factor MICAL1 binding to Myosin Va mediates cargo unloading during cytokinesis.
Authors: Niu, F. / Sun, K. / Wei, W. / Yu, C. / Wei, Z.
History
DepositionAug 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: Unconventional myosin-Va
B: Peptide from [F-actin]-monooxygenase MICAL1
C: Unconventional myosin-Va
D: Peptide from [F-actin]-monooxygenase MICAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2009
Polymers94,8904
Non-polymers3105
Water12,611700
1
A: Unconventional myosin-Va
B: Peptide from [F-actin]-monooxygenase MICAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6315
Polymers47,4452
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-0 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: Unconventional myosin-Va
D: Peptide from [F-actin]-monooxygenase MICAL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5694
Polymers47,4452
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-0 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.293, 63.220, 74.418
Angle α, β, γ (deg.)65.780, 86.710, 85.810
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Unconventional myosin-Va / / Dilute myosin heavy chain / non-muscle


Mass: 44404.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo5a, Dilute / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99104
#2: Protein/peptide Peptide from [F-actin]-monooxygenase MICAL1 / / Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 3040.421 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TDZ2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 121058 / % possible obs: 92.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Χ2: 2.899 / Net I/σ(I): 6.9 / Num. measured all: 542390
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.60.41854640.8270.2410.4850.46683.5
1.63-1.663.90.38658050.8590.2150.4440.47388.3
1.66-1.694.10.35359640.8910.1920.4040.47791.8
1.69-1.724.30.30761670.9270.1630.3490.49893.2
1.72-1.764.40.27260910.9430.1440.3090.51693.4
1.76-1.84.30.22460470.9540.120.2550.61892.2
1.8-1.854.50.19460520.9670.1020.220.74192.9
1.85-1.94.70.16261920.9770.0830.1820.69794.3
1.9-1.954.70.13561780.9820.0690.1520.70494.2
1.95-2.024.60.11361300.9860.0580.1270.95893.9
2.02-2.094.60.09561390.9890.0490.1071.0293
2.09-2.174.40.08158580.9920.0430.0910.99790.2
2.17-2.274.60.07461900.9930.0380.0831.68193.8
2.27-2.394.70.06661370.9930.0340.0751.50294.1
2.39-2.544.70.06261920.9940.0320.071.77294.3
2.54-2.744.60.05960900.9920.0310.0673.05692.7
2.74-3.014.60.05260630.9940.0270.0593.50292.3
3.01-3.454.80.04961890.9940.0250.0555.02595.1
3.45-4.344.60.04359580.9910.0230.0497.92590.9
4.34-504.80.04961520.9880.0250.05521.62493.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WB8

3wb8


Resolution: 1.6→50 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.1989 2014 1.67 %
Rwork0.1613 --
obs0.1619 120946 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.1 Å2 / Biso mean: 30.1714 Å2 / Biso min: 13.35 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 20 700 6918
Biso mean--51.82 42.39 -
Num. residues----773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0196465
X-RAY DIFFRACTIONf_angle_d1.7098760
X-RAY DIFFRACTIONf_chiral_restr0.1071016
X-RAY DIFFRACTIONf_plane_restr0.0091125
X-RAY DIFFRACTIONf_dihedral_angle_d13.9462533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6008-1.64080.27911240.2304720878
1.6408-1.68520.25321450.2137837991
1.6852-1.73480.21171340.1932862093
1.7348-1.79080.24451430.1861864693
1.7908-1.85480.20681430.1783853593
1.8548-1.92910.2051420.1692874294
1.9291-2.01680.20321590.1608868594
2.0168-2.12320.21031410.1563856093
2.1232-2.25620.17031490.1563852792
2.2562-2.43030.1871440.1536866794
2.4303-2.67490.19531510.1584868294
2.6749-3.06170.19241450.1591853592
3.0617-3.85680.18711530.1565869294
3.8568-37.07650.2071410.1566845491
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)
11.64690.10.33591.6139-0.19651.83710.06250.0119-0.0739-0.0494-0.0123-0.17480.23050.3667-00.18880.0253-0.01290.2014-0.02460.172120.5929-17.1219-1.9066
21.06970.06650.66510.06020.7921.31040.0134-0.1162-0.04020.09020.06320.07950.1474-0.1786-0.00010.2108-0.028-0.00210.17110.01190.19887.6018-17.4834-3.1981
32.121-0.54921.10740.5356-0.08220.740.02890.1803-0.0532-0.0337-0.04220.05460.01930.068100.189-0.010.00370.18310.00180.2124-8.0301-15.8009-28.3197
41.9788-0.1592-0.29211.6492-0.51750.224-0.12850.07280.21140.01240.0039-0.0301-0.0669-0.143800.20530.0329-0.01920.2561-0.01230.2747-25.4025-2.6975-30.1805
50.18550.36320.49630.48050.35191.2260.04860.0552-0.0663-0.0257-0.0092-0.11190.25710.1361-00.28310.0370.01810.23260.01160.242912.8117-20.8166-5.8068
60.2036-0.0645-0.01620.04240.05330.19540.0599-0.1841-0.16970.59960.0270.23610.1757-0.1915-00.3853-0.0668-0.01050.32980.03450.210111.9588-15.237916.815
70.01780.00170.05310.1390.05050.09690.1943-0.04350.1317-0.05480.0332-0.1488-0.55680.39460.00010.246-0.01810.05020.2660.02180.252512.3392-1.7281.9825
80.3549-0.0249-0.03830.2214-0.05290.2394-0.0214-0.1943-0.02310.24550.05630.23490.1392-0.436700.25350.00810.020.3148-0.0010.3496-1.6517-48.7846-23.5388
91.804-0.2473-0.0370.65410.72760.9213-0.04880.06070.2581-0.01330.09520.1073-0.2623-0.242100.20230.0280.01180.17430.00010.2435.3358-42.8771-24.233
100.80340.0276-0.03630.41410.4210.4508-0.08540.152-0.1527-0.21090.17860.17190.2421-0.235900.1862-0.0154-0.00490.18910.00080.20977.2639-52.3599-32.1034
111.38660.4116-0.20271.86010.32070.4797-0.0461-0.1178-0.01450.318-0.0044-0.1172-0.10770.1649-0.00030.18820.0028-0.00270.1412-0.01660.158215.4806-44.8155-20.4665
120.43290.0198-0.37160.29170.06530.0826-0.09390.12450.0035-0.14490.0401-0.09440.08650.030800.1977-0.0334-0.01470.2191-0.00180.169322.2057-41.6021-39.8993
130.925-0.15640.11940.51630.51740.56420.08780.17170.2686-0.1059-0.07470.0204-0.13880.044900.21580.00060.0230.21750.02620.241922.6387-25.3221-41.395
141.43780.36790.02481.4487-0.00080.21990.13470.1560.11460.0033-0.0272-0.0606-0.11030.019800.1727-0.01030.02180.21140.00040.19334.8633-27.1521-44.3617
151.9631-0.41390.62891.35860.43870.86930.03310.06660.2898-0.11010.0165-0.1475-0.04350.1885-00.2015-0.00830.03350.2385-0.00390.240749.0163-27.845-49.4907
160.2467-0.1856-0.02320.15760.1480.2406-0.15320.2033-0.33870.05890.19010.1890.2078-0.296200.2719-0.01290.07090.35820.05840.359455.5503-38.5438-54.0262
170.09330.46780.17730.8261-0.34870.6694-0.0546-0.04870.05440.04760.01280.0536-0.2119-0.0512-00.25440.0421-0.0150.1834-0.00340.193213.9797-40.5752-26.6279
180.2334-0.0203-0.01730.1861-0.1460.13270.062-0.3374-0.18070.3779-0.0643-0.07810.27930.27330.00130.311-0.0030.00260.25550.02030.216815.1956-61.5441-16.9417
190.0232-0.0155-0.03280.10410.07640.10170.00850.1748-0.141-0.56530.16830.29920.2707-0.0923-00.25540.0158-0.02440.2626-0.00770.242115.004-58.3357-36.7591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1471 through 1568 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1569 through 1627 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1628 through 1768 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1769 through 1815 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1816 through 1853 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 800 through 809 )B800 - 809
7X-RAY DIFFRACTION7chain 'B' and (resid 810 through 822 )B810 - 822
8X-RAY DIFFRACTION8chain 'C' and (resid 1471 through 1489 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 1490 through 1523 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 1524 through 1545 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 1546 through 1593 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 1594 through 1627 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1628 through 1679 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1680 through 1731 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1732 through 1795 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 1796 through 1815 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 1816 through 1853 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 800 through 809 )D800 - 809
19X-RAY DIFFRACTION19chain 'D' and (resid 810 through 822 )D810 - 822

+
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