[English] 日本語
Yorodumi
- PDB-4mzk: Crystal Structure of MTIP from Plasmodium falciparum in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mzk
TitleCrystal Structure of MTIP from Plasmodium falciparum in complex with pGly[807,811], a stapled myoA tail peptide
Components
  • Myosin A tail domain interacting protein
  • pGly[807,811], a stapled myoA tail peptide
KeywordsPROTEIN BINDING/inhibitor / Actomyosin motor / Stapled peptides / PROTEIN BINDING-inhibitor complex
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
pGly[807,811], a stapled myoA tail peptide / Myosin A tail domain interacting protein / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin A tail domain interacting protein
T: pGly[807,811], a stapled myoA tail peptide


Theoretical massNumber of molelcules
Total (without water)18,6762
Polymers18,6762
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.980, 55.030, 75.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Myosin A tail domain interacting protein


Mass: 16498.234 Da / Num. of mol.: 1 / Fragment: unp residues 61-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: MTIP, PFL2225w / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8I4W8
#2: Protein/peptide pGly[807,811], a stapled myoA tail peptide / PfM-A


Type: Peptide-like / Class: Inhibitor / Mass: 2177.744 Da / Num. of mol.: 1 / Fragment: unp residues 799-816 / Source method: obtained synthetically
Details: Synthesised peptide mimic of Plasmodium falciparum myosin A tail using Fmoc-Solid Phase Peptide Synthesis
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IDR3, pGly[807,811], a stapled myoA tail peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 807 AND NLE T 811 ARE CYCLIZED ...THE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 807 AND NLE T 811 ARE CYCLIZED THROUGH THEIR SIDE CHAINS AND A DOUBLE BOND INVOLVING CE ATOMS. SEE LINK RECORDS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir solution: 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate trihydrate, 30 % PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→37.98 Å / Num. all: 14866 / Num. obs: 14865 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.82-1.8713.40.783.81057199.9
8.14-37.989.90.02477209199.3

-
Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4AOM

4aom


Resolution: 1.82→37.915 Å / SU ML: 0.26 / σ(F): 1.49 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 754 5.08 %Random
Rwork0.18 ---
obs-14820 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.279 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 1.82→37.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 101 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071281
X-RAY DIFFRACTIONf_angle_d1.021727
X-RAY DIFFRACTIONf_dihedral_angle_d12.606474
X-RAY DIFFRACTIONf_chiral_restr0.071196
X-RAY DIFFRACTIONf_plane_restr0.003222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.88510.32281260.2722611X-RAY DIFFRACTION100
1.8851-1.96050.31510.21762601X-RAY DIFFRACTION100
1.9605-2.04980.22421500.19332610X-RAY DIFFRACTION100
2.0498-2.15780.25241590.19082597X-RAY DIFFRACTION100
2.1578-2.2930.23981350.18022625X-RAY DIFFRACTION100
2.293-2.470.26121350.18262622X-RAY DIFFRACTION100
2.47-2.71850.18951560.1812577X-RAY DIFFRACTION100
2.7185-3.11170.21331350.18152613X-RAY DIFFRACTION100
3.1117-3.91980.21781270.16752640X-RAY DIFFRACTION100
3.9198-37.92320.19511250.16442628X-RAY DIFFRACTION100
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)
15.1399-0.98251.63494.1463-1.20723.4345-0.25690.2871-1.19570.60120.15370.13930.8085-0.259-0.06270.4579-0.07410.05670.3378-0.00690.454114.5737-14.11835.4728
24.39061.9734-0.16143.7046-0.32772.5582-0.10250.295-0.2201-0.52870.047-0.19440.29490.07560.06550.21230.00560.0030.1491-0.01910.129521.5776-5.6423-4.9436
34.3272-0.0661-0.27462.53130.04223.3218-0.1182-0.03680.3616-0.12010.1168-0.0527-0.273-0.0423-0.0420.15580.00590.01070.12980.00310.150821.39580.83742.0621
42.1782-0.77030.4541.04310.49751.693-0.1537-0.2070.19860.14920.0344-0.03590.0562-0.06030.11070.15050.0066-0.02350.115-0.01140.153123.5421-1.548911.385
53.6842-0.225-0.19731.9129-0.06283.17290.15130.054-0.187-0.02810.0411-0.13550.36970.2201-0.18060.18250.0243-0.00160.134-0.00490.148724.7958-7.80695.3112
65.2007-0.8398-2.88871.88270.85362.1633-0.13520.0443-0.54990.2087-0.13620.31250.1478-0.17890.31230.1436-0.0040.02820.15780.01320.315610.5748-5.173815.1657
73.40960.48140.40044.22890.08913.7865-0.0793-0.3344-0.49020.35420.0171-0.16310.29820.16520.11040.1462-0.00870.02750.21210.01050.15754.04927.264622.4164
84.0325-1.55344.21392.2427-1.89584.4511-0.0172-1.716-0.13611.0720.47830.0554-0.1062-0.0046-0.18080.29650.06580.05240.5082-0.02980.2769-2.768315.924426.641
91.82560.1273-0.38510.87530.25831.04210.0290.01440.2592-0.0560.029-0.0802-0.1512-0.0202-0.00080.20850.01690.05510.1633-0.03250.20648.890516.716216.9435
104.64870.43730.69533.34810.50111.4948-0.13190.92720.6919-0.71220.36230.20350.0029-0.6820.15180.34470.01840.00320.38740.13310.19415.12417.24797.7005
113.98430.0157-0.34364.8351-0.49453.46930.00980.4546-0.2628-0.4454-0.07570.47130.232-0.3730.06580.1515-0.0319-0.03370.2209-0.03220.193-0.79868.498313.6789
123.88370.0181-0.07363.712-0.21125.80570.1343-0.0669-0.04040.03040.05380.1877-0.2371-0.1449-0.16650.11460.02140.02470.12310.00110.166111.76166.224714.535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 63:73 )A63 - 73
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:88 )A74 - 88
3X-RAY DIFFRACTION3( CHAIN A AND RESID 89:101 )A89 - 101
4X-RAY DIFFRACTION4( CHAIN A AND RESID 102:120 )A102 - 120
5X-RAY DIFFRACTION5( CHAIN A AND RESID 121:133 )A121 - 133
6X-RAY DIFFRACTION6( CHAIN A AND RESID 134:140 )A134 - 140
7X-RAY DIFFRACTION7( CHAIN A AND RESID 141:151 )A141 - 151
8X-RAY DIFFRACTION8( CHAIN A AND RESID 152:157 )A152 - 157
9X-RAY DIFFRACTION9( CHAIN A AND RESID 158:176 )A158 - 176
10X-RAY DIFFRACTION10( CHAIN A AND RESID 177:191 )A177 - 191
11X-RAY DIFFRACTION11( CHAIN A AND RESID 192:204 )A192 - 204
12X-RAY DIFFRACTION12( CHAIN T AND RESID 799:816 )T799 - 816

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more