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- PDB-5ce3: The Yersinia YopO - actin complex with MgADP -

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Basic information

Entry
Database: PDB / ID: 5ce3
TitleThe Yersinia YopO - actin complex with MgADP
Components
  • Actin
  • Protein kinase YopO
KeywordsCONTRACTILE PROTEIN/TRANSFERASE / Kinase cytoskeleton Pathogen host / CONTRACTILE PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site ...Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Actin / YopO
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLee, W.L. / Singaravelu, P. / Grimes, J.M. / Robinson, R.C.
Funding support Singapore, United Kingdom, 2items
OrganizationGrant numberCountry
Agency for Science, Technology and Research (A*STAR) Singapore
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: To Be Published
Title: The Yersinia YopO - actin complex with MgADP
Authors: Lee, W.L. / Grimes, J.M. / Robinson, R.C.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Actin
B: Protein kinase YopO
C: Actin
D: Protein kinase YopO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,06312
Polymers227,0654
Non-polymers1,9988
Water1629
1
A: Actin
B: Protein kinase YopO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5316
Polymers113,5322
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-42 kcal/mol
Surface area41900 Å2
MethodPISA
2
C: Actin
D: Protein kinase YopO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5316
Polymers113,5322
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-41 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.730, 121.750, 118.580
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALCYSCYSAA5 - 3746 - 375
21VALVALCYSCYSCC5 - 3746 - 375
12LYSLYSMETMETBB108 - 72922 - 643
22LYSLYSMETMETDD108 - 72922 - 643

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Actin /


Mass: 41755.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: G3CKA6
#2: Protein Protein kinase YopO / YopO


Mass: 71776.875 Da / Num. of mol.: 2 / Fragment: UNP residues 89-729 / Mutation: K205Y, E206Y, E207Y, K440Y, K441Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yopO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star / References: UniProt: Q93KQ6

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Non-polymers , 5 types, 17 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.35 Å3/Da / Density % sol: 63.3 % / Description: Thin plates
Crystal growTemperature: 279.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, pH 7.5, 30% PEG 400, 0.2M NaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.93→114.6 Å / Num. obs: 64212 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 63.37 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.9
Reflection shellResolution: 2.93→3.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX5.8.0107refinement
xia2data reduction
xia2data scaling
PHASERphasing
REFMAC5.8.0107refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CI6
Resolution: 2.93→114.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 35.703 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 6.361 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24024 3230 5.1 %RANDOM
Rwork0.19588 ---
obs0.19807 64212 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å22.88 Å2
2---9.7 Å2-0 Å2
3---8.68 Å2
Refinement stepCycle: 1 / Resolution: 2.93→114.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14992 0 120 9 15121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915408
X-RAY DIFFRACTIONr_bond_other_d0.0040.0214704
X-RAY DIFFRACTIONr_angle_refined_deg1.441.97520876
X-RAY DIFFRACTIONr_angle_other_deg1.168333904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79751902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68624.082686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.152152712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.57815104
X-RAY DIFFRACTIONr_chiral_restr0.0750.22350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117208
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0594.9917638
X-RAY DIFFRACTIONr_mcbond_other2.0594.9917637
X-RAY DIFFRACTIONr_mcangle_it3.4377.4859530
X-RAY DIFFRACTIONr_mcangle_other3.4377.4859531
X-RAY DIFFRACTIONr_scbond_it2.2655.2567770
X-RAY DIFFRACTIONr_scbond_other2.2655.2567771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8037.7811347
X-RAY DIFFRACTIONr_long_range_B_refined7.24847.1563642
X-RAY DIFFRACTIONr_long_range_B_other7.24847.14963639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A437860.07
12C437860.07
21B710880.09
22D710880.09
LS refinement shellResolution: 2.93→3.006 Å
RfactorNum. reflection% reflection
Rfree0.394 243 -
Rwork0.35 4437 -
obs--99.62 %
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)
11.1385-0.1734-0.44131.51820.26881.26240.03260.10230.2016-0.2980.015-0.2821-0.18040.1574-0.04760.0915-0.00220.02840.23640.02220.105962.155-30.493-9.725
20.47160.0774-0.00670.91590.07870.340.0231-0.0564-0.0490.1019-0.00680.28560.0621-0.1638-0.01630.1361-0.020.04050.39740.01150.162627.014-23.9229.502
31.0482-0.0902-0.54861.46940.10911.34290.06340.08220.1621-0.3068-0.0162-0.2288-0.15470.1403-0.04710.10170.02550.0250.22330.00960.0876101.486-32.43847.467
40.39770.1467-0.0520.78980.10590.35610.0331-0.059-0.04470.0823-0.02230.30210.0464-0.1756-0.01080.1357-0.02140.04480.39570.00210.203366.287-26.03466.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 374
2X-RAY DIFFRACTION2B108 - 729
3X-RAY DIFFRACTION3C5 - 374
4X-RAY DIFFRACTION4D108 - 729

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