PDB-7dhw: Crystal structure of myosin-XI motor domain in complex with ADP-ALF4

ID or keywords:

Entry

Database: PDB / ID: 7dhw

Title

Crystal structure of myosin-XI motor domain in complex with ADP-ALF4

Components

Motor domain of myosin

Keywords

MOTOR PROTEIN / Myosin / Motor domain / ATPase / ATP Binding

Function / homology

Function and homology information

microfilament motor activity => GO:0000146 / root hair elongation / vesicle transport along actin filament / myosin complex / microfilament motor activity / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.84 Å

Authors

Suzuki, K. / Haraguchi, T. / Tamanaha, M. / Yoshimura, K. / Imi, T. / Tominaga, M. / Sakayama, H. / Nishiyama, T. / Ito, K. / Murata, T.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of ultrafast myosin, its amino acid sequence, and structural features.
Authors: Haraguchi, T. / Tamanaha, M. / Suzuki, K. / Yoshimura, K. / Imi, T. / Tominaga, M. / Sakayama, H. / Nishiyama, T. / Murata, T. / Ito, K.

History

Deposition	Nov 17, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 19, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 13, 2021	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Feb 23, 2022	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3	Mar 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.4	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7dhw.cif.gz	364.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7dhw.ent.gz	247 KB	Display	PDB format
PDBx/mmJSON format	7dhw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7dhw_validation.pdf.gz	785 KB	Display	wwPDB validaton report
Full document	7dhw_full_validation.pdf.gz	799.4 KB	Display
Data in XML	7dhw_validation.xml.gz	27.3 KB	Display
Data in CIF	7dhw_validation.cif.gz	36.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/7dhw ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dhw	HTTPS FTP

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Related structure data

Related structure data	1mndS S: Starting model for refinement
Similar structure data	4k7z-1 6kgy-2 6kyy-1 1feb-d 6kod-2 6kod-1 2wp5-1 1nda-2 6kyy-2 6kgy-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (13) #174 - Jun 2014 GFP-like Proteins similarity (8) #172 - Apr 2014 RecA and Rad51 similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2) #168 - Dec 2013 DNA Helicase similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #26 - Feb 2002 Nitrogenase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #64 - Apr 2005 Kinesin similarity (1) #175 - Jul 2014 Microtubules similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#18 - Jun 2001
Myosin
similarity (13)
#174 - Jun 2014
GFP-like Proteins
similarity (8)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#243 - Mar 2020
Voltage-gated Sodium Channels
similarity (2)
#168 - Dec 2013
DNA Helicase
similarity (1)
#252 - Dec 2020
Hepatitis C Virus Protease/Helicase
similarity (1)
#26 - Feb 2002
Nitrogenase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#64 - Apr 2005
Kinesin
similarity (1)
#175 - Jul 2014
Microtubules
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Motor domain of myosin

hetero molecules

88.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.277, 73.725, 187.957
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 1 molecules A

#1: Protein	Motor domain of myosin / AtMYA2 Mass: 87476.922 Da / Num. of mol.: 1 / Fragment: UNP residues 1-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: XI-2, MYA2, At5g43900, F6B6.4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9LKB9

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Non-polymers , 5 types, 19 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ALF / TETRAFLUOROALUMINATE ION Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF₄
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.18 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT buffer (pH 6.0), 25% PEG-1500

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.84→19.81 Å / Num. obs: 19625 / % possible obs: 99.1 % / Redundancy: 5.58 % / B_iso Wilson estimate: 61.13 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.132 / R_rim(I) all: 0.147 / Net I/σ(I): 11.09

Reflection shell

Diffraction-ID: 1

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
7.9-19.81	0.028	40.75	951	0.999	0.032	92.3
2.84-3.01	0.84	2.1	2992	0.855	0.927
3.01-3.21	0.58	3.02	2927	0.906	0.642
3.21-3.46	0.357	5.01	2701	0.977	0.396	99.8
3.46-3.78	0.234	7.71	2487	0.983	0.261	99.4
3.78-4.21	0.131	11.42	2296	0.995	0.147	99.4
4.21-4.82	0.081	18.42	2063	0.997	0.09	100
4.82-5.82	0.072	19.1	1785	0.997	0.08	99.9
5.82-7.9	0.061	23.03	1424	0.997	0.068	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MND

1mnd

Resolution: 2.84→19.81 Å / SU ML: 0.4278 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5601 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2706	3642	10 %
R_work	0.2264	32779	-
obs	0.2309	19613	99.14 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 80.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.84→19.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5698	0	58	11	5767

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	5879
X-RAY DIFFRACTION	f_angle_d	0.49	7952
X-RAY DIFFRACTION	f_chiral_restr	0.0398	878
X-RAY DIFFRACTION	f_plane_restr	0.003	1031
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9682	3552

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.84-2.88	0.4558	127	0.3863	1156	X-RAY DIFFRACTION	90.61
2.88-2.92	0.4494	143	0.4018	1267	X-RAY DIFFRACTION	99.72
2.92-2.96	0.3728	138	0.3732	1256	X-RAY DIFFRACTION	99.86
2.96-3	0.42	132	0.3435	1245	X-RAY DIFFRACTION	99.49
3-3.05	0.3805	141	0.3356	1310	X-RAY DIFFRACTION	99.66
3.05-3.1	0.3195	140	0.3127	1228	X-RAY DIFFRACTION	99.78
3.1-3.15	0.3797	138	0.3109	1264	X-RAY DIFFRACTION	99.36
3.15-3.21	0.3549	147	0.2941	1306	X-RAY DIFFRACTION	99.52
3.21-3.27	0.3298	142	0.2812	1232	X-RAY DIFFRACTION	99.71
3.27-3.34	0.381	141	0.2854	1290	X-RAY DIFFRACTION	99.51
3.34-3.41	0.2779	141	0.2674	1256	X-RAY DIFFRACTION	99.71
3.41-3.49	0.2909	141	0.2525	1257	X-RAY DIFFRACTION	99.08
3.49-3.58	0.2845	144	0.246	1263	X-RAY DIFFRACTION	99.93
3.58-3.67	0.2453	140	0.2344	1278	X-RAY DIFFRACTION	98.95
3.67-3.78	0.2871	133	0.2278	1232	X-RAY DIFFRACTION	99.06
3.78-3.9	0.2966	143	0.2207	1285	X-RAY DIFFRACTION	98.76
3.9-4.04	0.2289	143	0.2072	1241	X-RAY DIFFRACTION	98.93
4.04-4.2	0.2939	147	0.199	1251	X-RAY DIFFRACTION	99.36
4.2-4.39	0.2627	139	0.1944	1268	X-RAY DIFFRACTION	99.72
4.39-4.62	0.2455	144	0.1704	1279	X-RAY DIFFRACTION	99.86
4.62-4.9	0.2242	142	0.1777	1293	X-RAY DIFFRACTION	99.93
4.9-5.27	0.2315	140	0.1901	1262	X-RAY DIFFRACTION	99.29
5.27-5.79	0.2381	140	0.2076	1263	X-RAY DIFFRACTION	99.72
5.79-6.6	0.263	140	0.2413	1269	X-RAY DIFFRACTION	100
6.6-8.22	0.2585	135	0.1931	1268	X-RAY DIFFRACTION	99.22
8.22-19.81	0.1651	141	0.1546	1260	X-RAY DIFFRACTION	99.01

Refinement TLS params.

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

ID	L11 (°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)
1	7.47571727661	-0.442721953124	-0.0682535822026	1.94720806774	-1.40833378569	1.60739827757	-0.383997144632	-0.973586233682	-0.756976594917	-0.469275114861	0.396464106519	-0.390827739586	0.1208083521	-0.505282488935	-0.125690087739	1.07631200506	-0.225132279497	0.108024606803	1.00302574475	-0.0184423781903	0.809599716847	-29.6878604423	-45.5928588974	-6.75548146783
2	5.3327970729	-0.158893148322	0.440811711872	3.68475842294	-0.449534256173	3.49696054498	0.123414822955	-0.0570803957839	-0.673700493105	0.319862107487	-0.0387478633695	-0.0445222636946	0.69936789705	0.0371631411051	-0.04585364687	0.611036137511	-0.0051406269675	0.0150992788515	0.28916128482	-0.0223305505449	0.480117269029	-3.49172637335	-47.0981633205	-16.1295455341
3	1.53984166599	0.894586201635	0.798213543782	2.5668504717	0.238642544232	1.5750131743	0.0284112081121	-0.0267679900628	-0.00511429415326	0.308329420855	0.031629596035	-0.211830828236	-0.17542271372	0.106545980712	-0.0968433281789	0.591342006887	0.00346375637727	0.0141219999274	0.352371351346	0.0431845089979	0.38923769978	12.087402782	-26.8966071889	-18.0414356611
4	1.30090279861	0.639854719463	0.211114297342	1.68116016615	0.492388954654	1.60137010919	-0.0695030488019	0.146115358786	0.273441102648	-0.192862130968	0.0296640962558	0.140220330479	-0.189784917755	0.0223009513514	0.015874586866	0.603489788937	0.0138799026997	-0.0371789110185	0.324831161303	0.0664409645966	0.345579540317	7.27793083936	-12.7511202399	-22.5878658179
5	4.19791418754	2.4134164948	0.00272286578131	4.90325379519	-0.663272460953	1.36082183541	-0.269920084445	0.289203373517	0.764143027666	0.410739943057	0.368048925257	0.473210876164	-0.0530550393201	-0.0738994650135	-0.0923629370599	0.981036786326	0.131602566824	-0.14729687879	0.639995106568	0.0263022716598	0.79868921348	-13.7393641867	-6.89051812772	-27.9243909999
6	2.75980244149	1.55357020018	2.02028806025	1.55034246524	1.03631869915	1.49295469936	-0.249742965798	0.337140025019	0.44745894509	-0.696669382707	0.213610055671	0.0867072750266	-0.483633123053	0.343428969513	0.128534621465	0.996466196272	-0.0421672322854	0.0222620571125	0.511554945866	0.0511165583187	0.621793673194	5.07696653545	-9.44673215152	-28.0371211159
7	0.576160769613	0.399019564299	0.631408318127	2.33967600636	-0.326981485773	2.08912714641	-0.207354890796	0.425884034753	-0.100206378687	-0.911381528925	0.124967341686	0.269764122492	0.306015127533	-0.250821766526	0.0254491771702	0.789050893368	-0.135175313005	-0.00885274217972	0.674388652167	-0.0459141912981	0.520426326537	-10.1799911426	-49.1724237525	-34.9077698702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 131 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 132 through 312 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 313 through 489 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 490 through 543 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 544 through 620 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 621 through 736 )

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