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- PDB-4mzl: Crystal Structure of MTIP from Plasmodium falciparum in complex w... -

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Basic information

Entry
Database: PDB / ID: 4mzl
TitleCrystal Structure of MTIP from Plasmodium falciparum in complex with HBS myoA, a hydrogen bond surrogate myoA helix mimetic
Components
  • Myosin A tail domain interacting protein
  • hydrogen bond surrogate (HBS) myoA helix mimetic
KeywordsPROTEIN BINDING/INHIBITOR / Actomyosin motor / Stapled peptides / PROTEIN BINDING-INHIBITOR complex / alpha-helix mimetic
Function / homology
Function and homology information


pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity ...pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / 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 ...: / Myosin A tail domain interacting protein, N-terminal / 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 domain interacting protein / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsDouse, C.H. / Garnett, J.A. / Maas, S.J. / Cota, E. / Tate, E.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Crystal Structures of Stapled and Hydrogen Bond Surrogate Peptides Targeting a Fully Buried Protein-Helix Interaction.
Authors: Douse, C.H. / Maas, S.J. / Thomas, J.C. / Garnett, J.A. / Sun, Y. / Cota, E. / Tate, E.W.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jun 7, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_fragment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_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 / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin A tail domain interacting protein
B: Myosin A tail domain interacting protein
C: hydrogen bond surrogate (HBS) myoA helix mimetic
D: hydrogen bond surrogate (HBS) myoA helix mimetic


Theoretical massNumber of molelcules
Total (without water)37,1584
Polymers37,1584
Non-polymers00
Water3,711206
1
A: Myosin A tail domain interacting protein
C: hydrogen bond surrogate (HBS) myoA helix mimetic


Theoretical massNumber of molelcules
Total (without water)18,5792
Polymers18,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-17 kcal/mol
Surface area8050 Å2
MethodPISA
2
B: Myosin A tail domain interacting protein
D: hydrogen bond surrogate (HBS) myoA helix mimetic


Theoretical massNumber of molelcules
Total (without water)18,5792
Polymers18,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.040, 58.650, 59.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 67:139 or resseq 142:204 ) and (not element H) and (not element D)
21chain A and (resseq 67:139 or resseq 142:204 ) and (not element H) and (not element D)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASPchain B and (resseq 66:139 or resseq 142:204 ) and (not element H) and (not element D)BB67 - 1398 - 80
12GLUGLUGLNGLNchain B and (resseq 66:139 or resseq 142:204 ) and (not element H) and (not element D)BB142 - 20483 - 145
21GLNGLNASPASPchain A and (resseq 66:139 or resseq 142:204 ) and (not element H) and (not element D)AA67 - 1398 - 80
22GLUGLUGLNGLNchain A and (resseq 66:139 or resseq 142:204 ) and (not element H) and (not element D)AA142 - 20483 - 145

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Components

#1: Protein Myosin A tail domain interacting protein


Mass: 16498.234 Da / Num. of mol.: 2 / Fragment: unp residues 61-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: PF3D7_1246400 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8I4W8
#2: Protein/peptide hydrogen bond surrogate (HBS) myoA helix mimetic


Mass: 2080.563 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IDR3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBUA AND 2JC REPRESENT THE CHEMICAL COMPONENTS FORMING THE HYDROGEN BOND SURROGATE (HBS) CYCLIC ...BUA AND 2JC REPRESENT THE CHEMICAL COMPONENTS FORMING THE HYDROGEN BOND SURROGATE (HBS) CYCLIC MOIETY STABILIZING A HELICAL PEPTIDE. BUA AND 2JC ARE COVALENTLY BONDED THROUGH A DOUBLE BOND INVOLVING ATOMS C1. SEE ALSO LINK RECORDS. THE BOND WAS FORMED BY A RING-CLOSING METATHESIS REACTION BETWEEN THE FUNCTIONALITY REPRESENTED BY BUA AND 2JC DURING SOLID-PHASE SYNTHESIS FORMING THE FINAL PRODUCT REPRESENTED BY THE MODELED COORDINATES OF CHAIN C AND D

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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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir solution: 0.2M MgCl2.(H2O)6 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→41.67 Å / Num. all: 22391 / Num. obs: 21734 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.01-2.125.10.2253092195
6.35-41.674.90.04812.8713196.1

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→41.668 Å / SU ML: 0.25 / σ(F): 1.07 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1109 5.12 %Random
Rwork0.1918 ---
obs-21686 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.149 Å2 / ksol: 0.323 e/Å3
Refinement stepCycle: LAST / Resolution: 2.01→41.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 206 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012454
X-RAY DIFFRACTIONf_angle_d1.1063302
X-RAY DIFFRACTIONf_dihedral_angle_d14.101880
X-RAY DIFFRACTIONf_chiral_restr0.074379
X-RAY DIFFRACTIONf_plane_restr0.004424
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1030X-RAY DIFFRACTIONPOSITIONAL0.072
12A1030X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0077-2.05440.30331250.21192520X-RAY DIFFRACTION91
2.0544-2.10580.31731590.2072644X-RAY DIFFRACTION95
2.1058-2.16270.29951580.19112567X-RAY DIFFRACTION94
2.1627-2.22630.23871210.22022624X-RAY DIFFRACTION93
2.2263-2.29820.33351370.26792583X-RAY DIFFRACTION93
2.2982-2.38030.25861310.20492657X-RAY DIFFRACTION95
2.3803-2.47560.28051680.18062604X-RAY DIFFRACTION94
2.4756-2.58830.24691170.19632614X-RAY DIFFRACTION94
2.5883-2.72470.22541500.17892625X-RAY DIFFRACTION93
2.7247-2.89540.25821540.19672606X-RAY DIFFRACTION96
2.8954-3.11880.27131360.2142741X-RAY DIFFRACTION96
3.1188-3.43260.30391280.20132701X-RAY DIFFRACTION97
3.4326-3.92890.21121450.18652663X-RAY DIFFRACTION96
3.9289-4.94880.16591470.14742695X-RAY DIFFRACTION96
4.9488-41.67740.17231510.18982592X-RAY DIFFRACTION94
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)
13.7620.6334-0.72421.80240.12352.80270.104-0.1683-0.30220.042-0.26870.05220.1722-0.41470.02150.13-0.0485-0.03990.27230.01010.100411.1984-0.3055-5.35
21.5921-0.236-1.2221.01770.01963.16540.03730.12580.1001-0.03190.0196-0.0557-0.3420.07490.04820.12550.0109-0.05220.1403-0.02030.061718.34784.2666-0.8199
31.5547-0.5014-0.32280.18960.28251.1755-0.0380.22830.12720.00540.0632-0.0819-0.05380.04820.00960.0745-0.0146-0.03780.0672-0.02750.083325.386-2.03271.5792
41.0627-0.1741-0.35190.12760.08441.923-0.0670.184-0.17550.0413-0.03850.02630.14260.05130.05850.1315-0.02830.00810.124-0.03370.092719.3609-5.8142-0.1358
52.613-0.84460.56180.665-0.24792.9262-0.0070.0063-0.2184-0.15320.0848-0.01080.14410.1925-0.02390.10240.0405-0.00510.07810.02330.06721.9557-4.703425.0594
62.05240.2737-1.22130.892-0.15822.072-0.0616-0.29220.00880.0717-0.0594-0.09490.1140.18260.11330.08560.0042-0.0310.0509-0.00140.078622.28694.699626.2818
71.1505-0.0101-0.19321.8024-0.1891.7996-0.0269-0.01060.16840.0928-0.0491-0.0461-0.0886-0.20490.0730.0610.0066-0.00360.0844-0.00650.113613.11655.156423.1037
80.7101-0.36760.40650.2912-0.090.3763-0.0565-0.00330.09470.01360.02420.0423-0.0497-0.027-0.02720.39630.20590.06760.29130.15110.360233.37524.131240.8973
93.2352-0.51190.22842.1692-0.83583.3526-0.0787-0.2276-0.19320.1304-0.10130.14220.0743-0.1409-0.0560.1008-0.02840.07860.0751-0.04080.071534.7194-6.314747.6708
101.39340.4239-0.85650.6376-0.19531.0156-0.1457-0.2438-0.28920.0732-0.0785-0.00760.15490.120.0520.11550.0350.04990.04080.01320.117342.5937-7.561942.1013
110.5505-0.12960.38960.73671.06314.9939-0.1643-0.2187-0.05720.0460.07560.1190.05880.33740.05390.05040.01850.01520.10380.01480.147753.0455-1.333940.6442
121.69530.30970.38590.6695-0.40172.95010.0118-0.15290.083-0.0133-0.238-0.1482-0.07950.11240.14920.10390.00430.00320.06190.00280.116244.55990.71942.2121
131.60380.6036-0.44020.7571-0.25081.5808-0.04690.13910.0313-0.00710.07460.028-0.0490.35550.04260.1323-0.0608-0.03170.26660.09510.209146.64890.560916.2289
141.8294-0.08021.19640.634-0.37071.958-0.16620.49770.1603-0.1582-0.0187-0.0955-0.12010.16080.12010.1539-0.00060.02640.17740.01720.121546.9869-8.286514.973
151.21290.04930.61032.0032-0.80281.84910.0210.16050.079-0.1308-0.0983-0.04360.0768-0.13640.10530.06870.01530.02350.10670.00830.11437.7201-8.738518.1386
162.58660.9010.42021.6820.39532.4391-0.06480.0831-0.0206-0.0942-0.0021-0.0231-0.1064-0.27930.01130.06040.0055-0.00090.0716-0.00960.053420.10120.964514.5591
171.3016-0.2594-0.32551.42360.0350.9622-0.03270.0171-0.0807-0.0223-0.0659-0.00370.04350.00970.00030.0660.03160.0097-0.00260.01330.059244.4492-4.894226.7233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 67:88)
2X-RAY DIFFRACTION2chain 'A' and (resseq 89:101)
3X-RAY DIFFRACTION3chain 'A' and (resseq 102:120)
4X-RAY DIFFRACTION4chain 'A' and (resseq 121:140)
5X-RAY DIFFRACTION5chain 'A' and (resseq 141:151)
6X-RAY DIFFRACTION6chain 'A' and (resseq 152:176)
7X-RAY DIFFRACTION7chain 'A' and (resseq 177:204)
8X-RAY DIFFRACTION8chain 'B' and (resseq 67:73)
9X-RAY DIFFRACTION9chain 'B' and (resseq 74:84)
10X-RAY DIFFRACTION10chain 'B' and (resseq 85:107)
11X-RAY DIFFRACTION11chain 'B' and (resseq 108:118)
12X-RAY DIFFRACTION12chain 'B' and (resseq 119:140)
13X-RAY DIFFRACTION13chain 'B' and (resseq 141:151)
14X-RAY DIFFRACTION14chain 'B' and (resseq 152:176)
15X-RAY DIFFRACTION15chain 'B' and (resseq 177:204)
16X-RAY DIFFRACTION16chain 'C' and (resseq 800:816)
17X-RAY DIFFRACTION17chain 'D' and (resseq 800:816)

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