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- PDB-2auc: Structure of the Plasmodium MTIP-MyoA complex, a key component of... -

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Basic information

Entry
Database: PDB / ID: 2auc
TitleStructure of the Plasmodium MTIP-MyoA complex, a key component of the parasite invasion motor
Components
  • Myosin A
  • Myosin A Tail Interacting Protein
KeywordsMEMBRANE PROTEIN / SGPP / Structural GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE MTIP / MyoA / myosin A-tail / MyoA Tail Interacting Protein / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


vesicle transport along actin filament / myosin complex / microfilament motor activity / actin filament organization / actin filament binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. ...Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin A Tail Interacting Protein / Myosin-A
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBosch, J. / Turley, S. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of the MTIP-MyoA complex, a key component of the malaria parasite invasion motor.
Authors: Bosch, J. / Turley, S. / Daly, T.M. / Bogh, S.M. / Villasmil, M.L. / Roach, C. / Zhou, N. / Morrisey, J.M. / Vaidya, A.B. / Bergman, L.W. / Hol, W.G.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 15.09 (9.18 B<40) BAD ROTAMERS : 9.0% 25/277 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 4.4% 14/318 (TARGET 0.2%) RAMACHANDRAN FAVORED : 85.8% 273/318 (TARGET 98.0%)
Remark 999SEQUENCE The sequence of myosin A tail domain interacting protein is not available at SWS and ...SEQUENCE The sequence of myosin A tail domain interacting protein is not available at SWS and Gebank databases at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin A Tail Interacting Protein
B: Myosin A Tail Interacting Protein
C: Myosin A Tail Interacting Protein
D: Myosin A


Theoretical massNumber of molelcules
Total (without water)46,2814
Polymers46,2814
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.239, 95.239, 87.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Myosin A Tail Interacting Protein / MTIP


Mass: 14812.686 Da / Num. of mol.: 3 / Fragment: myosin A tail domain interacting protein MTIP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D0VWV5*PLUS
#2: Protein/peptide Myosin A / MyoA


Mass: 1843.290 Da / Num. of mol.: 1 / Fragment: myosin A / Source method: obtained synthetically
Details: The sequence of this peptide naturally exists in Plasmodium yoelli
References: UniProt: Q7RQ71*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.6 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 20 % w/v PEG200, 0.05 M sodium acetate pH5.3, 1 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97953 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 13219 / % possible obs: 99.91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rsym value: 0.149 / Net I/σ(I): 21.1
Reflection shellResolution: 2.6→2.739 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.868 / SU B: 29.053 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.993 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES 156 - 159, 183, 185, 188, 189 OF CHAIN B WERE MODELED WITHOUT SIDE CHAINS AS NO SIDE CHAIN DENSITY IS OBSERVABLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.28326 693 5 %RANDOM
Rwork0.22658 ---
obs0.22938 13219 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.113 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 0 71 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9391.9544033
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82325.155161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01315564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4481518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022271
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.21296
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2860.22099
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04541874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4962905
X-RAY DIFFRACTIONr_scbond_it1.59261269
X-RAY DIFFRACTIONr_scangle_it2.489101127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.739 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.383 106 -
Rwork0.267 1897 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.8660.38790.24948.5217-0.26018.7921-0.2551-0.0864-0.10550.08660.47440.1069-0.27650.3807-0.2194-0.0496-0.0024-0.018-0.01920.0337-0.115261.2316-3.06217.7353
218.3013-1.79811.88452.4051-0.62410.2805-0.02690.30790.0028-0.3392-0.05020.06370.10110.49730.0771-0.0085-0.03430.01780.05040.0824-0.092961.2788-3.06039.0198
339.20233.5811-1.67864.377-4.06087.71790.2545-0.07540.17-0.192-0.0777-0.1139-0.3945-0.3442-0.17680.06890.03810.0449-0.15360.1057-0.018937.6746-7.11787.104
427.7073-17.05923.170725.5772-4.07687.08120.77550.19890.9410.1167-0.60650.7565-0.5813-0.0124-0.169-0.085-0.10670.14530.01070.08840.03929.703-11.458614.8907
55.91483.3365-3.54518.1534-6.52469.7341-0.2189-0.2197-0.501-0.10270.0974-0.44-0.2426-0.30360.1215-0.0563-0.0235-0.03-0.0683-0.0520.045140.115-16.15876.6916
610.2388-1.5615-13.3720.31630.78337.67180.8071-1.394-1.2567-0.0602-0.518-1.06531.00491.0838-0.2891-0.0976-0.184-0.11390.02120.22580.112145.3246-19.661114.7196
75.8116-3.06572.336113.2774-4.832513.80620.0981-0.46870.64512.1771-0.5887-0.9343-1.73350.12620.49060.1321-0.2522-0.0856-0.03470.0749-0.038838.5-10.827218.8777
80.4604-1.9753-0.864910.27240.34567.928-0.31370.68070.4969-0.45070.036-0.8683-0.10130.3680.2777-0.11990.02880.03060.0472-0.02510.071140.764410.9387-17.8207
99.4505-9.66482.753111.9529-8.926218.84950.0446-0.2705-1.9854-0.2834-0.05550.07660.16260.57440.0109-0.03270.1790.1004-0.2722-0.12170.025740.40581.7849-13.8641
103.11465.1632.565716.13360.5083.9652-0.00220.31730.1011-0.52040.23540.5960.0182-0.1566-0.2332-0.00990.0325-0.0001-0.05940.001-0.023231.017910.9492-14.7303
112.8705-5.41730.286410.5398-1.55863.3072-0.28950.0868-0.08360.56260.1584-0.23050.1834-0.22360.1310.06550.0462-0.0267-0.04880.0011-0.033138.05039.3288-7.2158
124.23470.6945.307745.3423-6.70377.92080.32160.18270.0085-0.3715-0.15810.10590.67710.2616-0.16360.079-0.05220.0055-0.0711-0.019-0.118338.277-11.1211-5.0633
1319.96550.1969-5.04932.1686-18.677312.0639-0.22811.6461-2.7232-2.0705-0.9927-0.99242.33751.76461.22080.43330.1650.2512-0.1595-0.29040.049334.7121-24.4552-8.9011
142.3244-4.9745.672120.24946.695750.77220.5414-0.3693-1.4924-0.5037-0.13890.4405-0.7351-0.717-0.4025-0.328-0.2951-0.02330.03480.21650.07526.4586-18.2146-4.1531
1516.72186.60432.92832.82244.160642.6727-0.87790.0587-0.76190.11940.51451.0192-1.03950.01240.36340.0565-0.0474-0.1393-0.0440.10690.07123.1823-11.5565-10.6157
1615.1431-16.3462.825356.8082-21.22298.96010.60640.43730.0387-1.27690.371-0.42450.66640.5876-0.97740.4024-0.0414-0.0725-0.0692-0.273-0.166536.023-12.7456-14.1301
1745.2427-8.68151.736737.5289-8.41181.8865-0.0332-2.00750.15030.0125-0.60310.0746-1.3045-0.99170.6362-0.03140.04090.06470.03080.0904-0.257330.5899-2.47711.4629
181.8151-3.24852.473610.42851.758311.6615-0.1327-0.3791-1.08630.34930.16150.62870.1035-0.5511-0.0288-0.1181-0.05030.0057-0.02030.18820.044145.44627.11625.421
1919.23871.29744.833213.20110.77085.73360.4975-0.90660.70191.58140.11810.29540.0088-0.2047-0.61560.03430.02790.0623-0.0241-0.0578-0.126443.332116.135111.3639
2022.1867-3.2149-11.09343.19117.799619.6161-0.0914-0.82680.48950.39790.1678-0.1825-1.00470.1403-0.07640.05890.0268-0.0111-0.13590.0451-0.00243.740516.06972.9018
2143.2445-7.4465-14.25596.297-0.058112.4785-0.0294-0.1849-0.8014-0.2898-0.0401-0.03120.4369-0.07490.06940.0737-0.0522-0.0308-0.2362-0.0017-0.078159.985213.1103-6.2339
224.8646-2.37540.300412.2607-0.100110.5113-0.27240.128-0.8048-0.66130.2358-0.80010.69970.45240.0366-0.06270.07810.0589-0.14530.05490.041475.62429.3309-7.6653
238.5106-0.26742.55626.0084-0.68233.9956-0.1262-0.3634-0.674-0.0927-0.0611-0.34790.40980.13160.1873-0.00840.03220.0563-0.06950.1283-0.028873.67198.11891.9166
2410.186-2.65630.07476.15654.144417.8753-0.8256-0.4699-0.02350.7808-0.23850.1358-0.2595-0.2711.064-0.0185-0.0682-0.0658-0.11550.0930.023469.068717.5844.1878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA88 - 11710 - 39
2X-RAY DIFFRACTION2AA118 - 14040 - 62
3X-RAY DIFFRACTION3AA141 - 15263 - 74
4X-RAY DIFFRACTION4AA153 - 16275 - 84
5X-RAY DIFFRACTION5AA163 - 17685 - 98
6X-RAY DIFFRACTION6AA177 - 18899 - 110
7X-RAY DIFFRACTION7AA189 - 203111 - 125
8X-RAY DIFFRACTION8BB89 - 10111 - 23
9X-RAY DIFFRACTION9BB102 - 11024 - 32
10X-RAY DIFFRACTION10BB111 - 12433 - 46
11X-RAY DIFFRACTION11BB125 - 13747 - 59
12X-RAY DIFFRACTION12BB138 - 15160 - 73
13X-RAY DIFFRACTION13BB152 - 16274 - 84
14X-RAY DIFFRACTION14BB163 - 17385 - 95
15X-RAY DIFFRACTION15BB174 - 18996 - 111
16X-RAY DIFFRACTION16BB195 - 204117 - 126
17X-RAY DIFFRACTION17CC79 - 851 - 7
18X-RAY DIFFRACTION18CC89 - 10911 - 31
19X-RAY DIFFRACTION19CC115 - 12537 - 47
20X-RAY DIFFRACTION20CC126 - 13548 - 57
21X-RAY DIFFRACTION21CC136 - 14958 - 71
22X-RAY DIFFRACTION22CC150 - 17372 - 95
23X-RAY DIFFRACTION23CC174 - 20496 - 126
24X-RAY DIFFRACTION24DD803 - 8161 - 14

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