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- PDB-6ixp: Structure of Myo2-GTD in complex with Mmr1 -

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Basic information

Entry
Database: PDB / ID: 6ixp
TitleStructure of Myo2-GTD in complex with Mmr1
Components
  • Mitochondrial MYO2 receptor-related protein 1
  • Myosin-2
KeywordsPROTEIN BINDING/CELL CYCLE / Cargo binding domain / PROTEIN BINDING / PROTEIN BINDING-CELL CYCLE complex
Function / homology
Function and homology information


peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / cellular bud ...peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / cellular bud / vacuole inheritance / vesicle transport along actin filament / incipient cellular bud site / cellular bud tip / cortical endoplasmic reticulum / Golgi inheritance / cellular bud neck / mating projection tip / fungal-type vacuole membrane / vesicle docking involved in exocytosis / microfilament motor activity / actin filament bundle / filamentous actin / intracellular distribution of mitochondria / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / actin filament organization / phospholipid binding / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / vesicle / mitochondrial outer membrane / calmodulin binding / cell division / mitochondrion / ATP binding / membrane / cytoplasm
Similarity search - Function
Mitochondrial Myo2 receptor-related protein 1 / Mitochondrial Myo2 receptor-related protein / : / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Mitochondrial Myo2 receptor-related protein 1 / Mitochondrial Myo2 receptor-related protein / : / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-2 / Mitochondrial MYO2 receptor-related protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.733 Å
AuthorsTang, K. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.
Authors: Tang, K. / Li, Y. / Yu, C. / Wei, Z.
History
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-2
B: Mitochondrial MYO2 receptor-related protein 1
C: Mitochondrial MYO2 receptor-related protein 1
D: Myosin-2
E: Mitochondrial MYO2 receptor-related protein 1
F: Mitochondrial MYO2 receptor-related protein 1


Theoretical massNumber of molelcules
Total (without water)112,4586
Polymers112,4586
Non-polymers00
Water724
1
A: Myosin-2
B: Mitochondrial MYO2 receptor-related protein 1
C: Mitochondrial MYO2 receptor-related protein 1


Theoretical massNumber of molelcules
Total (without water)56,2293
Polymers56,2293
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-23 kcal/mol
Surface area20340 Å2
MethodPISA
2
D: Myosin-2
E: Mitochondrial MYO2 receptor-related protein 1
F: Mitochondrial MYO2 receptor-related protein 1


Theoretical massNumber of molelcules
Total (without water)56,2293
Polymers56,2293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-22 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.387, 63.459, 169.077
Angle α, β, γ (deg.)90.000, 104.720, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASPASPchain AAA1152 - 15725 - 419
21ASNASNASPASPchain DDD1152 - 15725 - 419
12ILEILELEULEUchain BBB403 - 41812 - 27
22ILEILELEULEUchain EEE403 - 41812 - 27
13THRTHRPROPROchain CCC408 - 42517 - 34
23THRTHRPROPROchain FFF408 - 42517 - 34

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Myosin-2 / Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain ...Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2


Mass: 47961.508 Da / Num. of mol.: 2 / Mutation: Deletions 1342-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MYO2, CDC66, YOR326W, O6167 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19524
#2: Protein/peptide
Mitochondrial MYO2 receptor-related protein 1 / Mmr1


Mass: 4133.644 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MMR1, YLR190W / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06324
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3350 and 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.73→54.55 Å / Num. obs: 28335 / % possible obs: 93.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 71.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 8.1 / Num. measured all: 192730
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.73-2.887.21.1363189044040.9270.4531.2242.899.6
8.64-54.556.20.035624810130.9980.0150.03915.898.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6H

2f6h


Resolution: 2.733→53.381 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1316 4.68 %
Rwork0.2423 26815 -
obs0.2443 28131 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 246.7 Å2 / Biso mean: 106.1384 Å2 / Biso min: 49.58 Å2
Refinement stepCycle: final / Resolution: 2.733→53.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 0 4 6782
Biso mean---81.45 -
Num. residues----844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046921
X-RAY DIFFRACTIONf_angle_d0.719406
X-RAY DIFFRACTIONf_chiral_restr0.0261121
X-RAY DIFFRACTIONf_plane_restr0.0031173
X-RAY DIFFRACTIONf_dihedral_angle_d12.832538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3720X-RAY DIFFRACTION5.169TORSIONAL
12D3720X-RAY DIFFRACTION5.169TORSIONAL
21B136X-RAY DIFFRACTION5.169TORSIONAL
22E136X-RAY DIFFRACTION5.169TORSIONAL
31C182X-RAY DIFFRACTION5.169TORSIONAL
32F182X-RAY DIFFRACTION5.169TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7326-2.8420.42471440.37453152329699
2.842-2.97140.37721730.35423126329998
2.9714-3.1280.38531360.34223153328998
3.128-3.3240.37321330.31213191332499
3.324-3.58060.35761230.29322403252675
3.5806-3.94080.30311120.27142332244472
3.9408-4.51080.25571580.21843134329298
4.5108-5.68210.29061690.21273069323896
5.6821-53.39090.22051680.19173255342398
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)
12.1257-0.17011.96372.335-2.21657.28840.11-0.3628-0.26-0.57010.1450.55550.5774-0.9826-0.2740.4204-0.02990.00620.65040.03070.70814.9445-17.2615-3.2816
23.2762-0.29340.47593.68540.50356.7269-0.119-1.06630.18440.87150.1181-0.1048-0.892-0.2773-0.03550.74860.05340.06310.9776-0.05830.673833.3887-14.460934.9795
31.447-0.33110.04211.8170.39585.0330.1667-0.063-0.2752-0.5917-0.08570.3524-0.1004-0.0402-0.02480.84290.10360.00030.78260.06280.921520.8585-18.3194-1.8343
49.79256.55325.96135.21084.37933.8137-0.58160.64940.74010.1209-0.3831-1.1355-0.73770.98380.74781.9192-0.1997-0.21651.02390.05571.38829.1145-12.6184-26.2202
54.8272-1.0416-0.98984.77060.7042.24760.60110.860.2318-0.83220.24410.26630.17010.0812-0.58521.12560.08580.02430.80410.18850.810920.5092-12.8932-18.5347
63.5303-5.45291.00848.5457-1.57280.2882-0.0631-0.09291.1639-0.2555-0.0126-0.98041.1685-1.17480.15691.73620.1045-0.25410.6715-0.23330.909427.6789-27.0913-17.329
74.74220.8887-2.45139.0259-1.81621.47380.0295-0.20320.571-0.82260.89890.2173-0.8373-2.3325-0.76120.71360.37060.2531.61570.1380.85628.1695-8.00966.9126
83.26741.58360.12665.02390.19842.6567-0.023-0.5955-0.67740.2619-0.04920.4607-0.1995-2.0039-0.07460.99710.02860.15321.7829-0.04041.26619.1899-16.469820.8667
96.4704-0.67671.90446.2666-0.40237.68890.3761-0.2009-0.40410.2695-0.3117-0.08010.78460.413-0.31161.13570.0716-0.03820.72430.18020.788174.4253-26.104292.1757
101.954-0.30372.33482.04121.01187.3222-0.1954-0.00450.14590.24740.0143-0.0287-0.14770.88570.1210.7419-0.06290.020.82880.01980.796573.6676-15.940280.6438
112.9825-0.3416-0.32471.5881-0.83739.82890.1814-0.1203-0.21460.5294-0.1139-0.17551.27180.05670.02161.03780.0167-0.09440.62310.06160.920657.6919-27.568462.2406
122.0393-0.90161.92642.3026-0.85897.0434-0.12210.0623-0.0393-0.2584-0.0160.0843-0.10240.28720.13491.0135-0.0062-0.01540.6705-0.05630.807856.642-14.204444.0632
131.43350.29860.68931.68220.42844.87110.1384-0.3264-0.1484-0.3324-0.18610.16390.9482-0.2527-0.00451.1834-0.0476-0.0320.83430.09030.95667.6868-24.36993.2738
146.4864-4.50233.93568.5256-4.44135.5043-0.2644-0.63871.1614-0.1139-0.42630.27120.47430.70830.40721.987-0.0615-0.1831.26170.0521.258579.7664-15.1622108.2676
154.09561.5608-2.62145.7187-0.782.18610.05560.3617-0.0674-0.0091-0.42940.11610.5134-0.45880.16741.4240.0371-0.08010.9953-0.04080.855168.3337-14.9066100.1798
160.33830.5350.06060.84370.08850.00740.69180.63130.4233-0.35910.03820.98331.1243-0.1721-0.30371.0393-0.0936-0.2690.68310.50551.287161.0816-27.930999.1648
177.0182-0.5241-0.91639.43970.32311.97040.4449-0.00820.36010.24751.786-0.0563-1.04670.9386-2.07450.9965-0.2350.03760.9843-0.05490.870780.8863-10.590674.8161
183.8406-1.8771-0.09558.33420.7073.5510.16711.3655-0.545-0.8442-0.5764-0.8259-0.68122.45550.41211.0085-0.1020.17511.73060.0861.002379.8569-19.210260.8448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1152 through 1325 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1326 through 1504 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1505 through 1572 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 403 through 407 )B403 - 407
5X-RAY DIFFRACTION5chain 'B' and (resid 408 through 412 )B408 - 412
6X-RAY DIFFRACTION6chain 'B' and (resid 413 through 418 )B413 - 418
7X-RAY DIFFRACTION7chain 'C' and (resid 408 through 414 )C408 - 414
8X-RAY DIFFRACTION8chain 'C' and (resid 415 through 425 )C415 - 425
9X-RAY DIFFRACTION9chain 'D' and (resid 1152 through 1217 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 1218 through 1325 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 1326 through 1375 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 1376 through 1532 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 1533 through 1572 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 403 through 407 )E403 - 407
15X-RAY DIFFRACTION15chain 'E' and (resid 408 through 412 )E408 - 412
16X-RAY DIFFRACTION16chain 'E' and (resid 413 through 418 )E413 - 418
17X-RAY DIFFRACTION17chain 'F' and (resid 408 through 414 )F408 - 414
18X-RAY DIFFRACTION18chain 'F' and (resid 415 through 425 )F415 - 425

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