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- PDB-6ku0: Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM -

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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


establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / hippocampal mossy fiber expansion / : / melanosome localization / endoplasmic reticulum localization / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation ...establishment of endoplasmic reticulum localization to postsynapse / regulation of postsynaptic cytosolic calcium ion concentration / hippocampal mossy fiber expansion / : / melanosome localization / endoplasmic reticulum localization / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / locomotion involved in locomotory behavior / melanin metabolic process / regulation of regulated secretory pathway / vesicle transport along actin filament / unconventional myosin complex / insulin-responsive compartment / NAD(P)H oxidase H2O2-forming activity / developmental pigmentation / secretory granule localization / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of actin dynamics for phagocytic cup formation / actin filament-based movement / 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 / hair follicle maturation / melanin biosynthetic process / melanocyte differentiation / melanosome transport / actomyosin / actin filament depolymerization / myosin complex / intermediate filament / odontogenesis / long-chain fatty acid biosynthetic process / insulin secretion / microfilament motor activity / pigmentation / exocytosis / cytoskeletal motor activity / actin filament bundle assembly / photoreceptor outer segment / smooth endoplasmic reticulum / intercellular bridge / vesicle-mediated transport / cytoskeleton organization / myelination / visual perception / FAD binding / secretory granule / protein localization to plasma membrane / actin filament / monooxygenase activity / synapse organization / SH3 domain binding / small GTPase binding / cellular response to insulin stimulus / disordered domain specific binding / actin filament binding / melanosome / actin cytoskeleton / actin binding / Factors involved in megakaryocyte development and platelet production / midbody / chemical synaptic transmission / endosome membrane / calmodulin binding / postsynapse / ciliary basal body / cilium / neuronal cell body / calcium ion binding / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / Golgi apparatus / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain ...Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / 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 / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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