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- PDB-6hyq: Regulatory subunit of a cAMP-independent protein kinase A from Tr... -

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Basic information

Entry
Database: PDB / ID: 6hyq
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma cruzi bound to guanosine
ComponentsProtein kinase A regulatory subunit
KeywordsSIGNALING PROTEIN / protein kinase A / regulatory subunit / cell signalling
Function / homology
Function and homology information


cilium / kinase activity / phosphorylation
Similarity search - Function
Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
ACETATE ION / GUANOSINE / Protein kinase A regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBo1100/7-1 Germany
CitationJournal: to be published
Title: Regulatory subunit of a cAMP-independent protein kinase A from Trypanosoma cruzi in complex with guanosine
Authors: Volpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Protein kinase A regulatory subunit
B: Protein kinase A regulatory subunit
C: Protein kinase A regulatory subunit
D: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,22913
Polymers137,9044
Non-polymers2,3259
Water3,117173
1
A: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0433
Polymers34,4761
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1024
Polymers34,4761
Non-polymers6263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0433
Polymers34,4761
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0433
Polymers34,4761
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.910, 80.819, 149.343
Angle α, β, γ (deg.)90.000, 92.799, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
12TYRTYRILEILE(chain A and ((resid 220 and (name N or name...AA220 - 23521 - 36
13LYSLYSILEILE(chain A and ((resid 220 and (name N or name...AA237 - 25338 - 54
14VALVALALAALA(chain A and ((resid 220 and (name N or name...AA255 - 25956 - 60
15GLNGLNALAALA(chain A and ((resid 220 and (name N or name...AA261 - 27462 - 75
16THRTHRTYRTYR(chain A and ((resid 220 and (name N or name...AA277 - 28378 - 84
17ILEILEGLUGLU(chain A and ((resid 220 and (name N or name...AA285 - 29586 - 96
18LYSLYSLEULEU(chain A and ((resid 220 and (name N or name...AA298 - 31399 - 114
19TYRTYRTYRTYR(chain A and ((resid 220 and (name N or name...AA315116
110THRTHRASNASN(chain A and ((resid 220 and (name N or name...AA317 - 342118 - 143
111VALVALPHEPHE(chain A and ((resid 220 and (name N or name...AA344 - 385145 - 186
112PROPROTYRTYR(chain A and ((resid 220 and (name N or name...AA387 - 394188 - 195
113GLYGLYLEULEU(chain A and ((resid 220 and (name N or name...AA398 - 401199 - 202
114ILEILEVALVAL(chain A and ((resid 220 and (name N or name...AA403 - 411204 - 212
115GLYGLYMETMET(chain A and ((resid 220 and (name N or name...AA413 - 465214 - 266
116PROPROLYSLYS(chain A and ((resid 220 and (name N or name...AA469 - 475270 - 276
117CYSCYSSERSER(chain A and ((resid 220 and (name N or name...AA477 - 498278 - 299
218TYRTYRILEILE(chain B and ((resid 220 and (name N or name...BB220 - 23521 - 36
219LYSLYSILEILE(chain B and ((resid 220 and (name N or name...BB237 - 25338 - 54
220VALVALALAALA(chain B and ((resid 220 and (name N or name...BB255 - 25956 - 60
221GLNGLNALAALA(chain B and ((resid 220 and (name N or name...BB261 - 27462 - 75
222THRTHRTYRTYR(chain B and ((resid 220 and (name N or name...BB277 - 28378 - 84
224ILEILEGLUGLU(chain B and ((resid 220 and (name N or name...BB285 - 29586 - 96
225LYSLYSLEULEU(chain B and ((resid 220 and (name N or name...BB298 - 31399 - 114
226TYRTYRTYRTYR(chain B and ((resid 220 and (name N or name...BB315116
227THRTHRASNASN(chain B and ((resid 220 and (name N or name...BB317 - 342118 - 143
228VALVALPHEPHE(chain B and ((resid 220 and (name N or name...BB344 - 385145 - 186
229PROPROTYRTYR(chain B and ((resid 220 and (name N or name...BB387 - 394188 - 195
230GLYGLYLEULEU(chain B and ((resid 220 and (name N or name...BB398 - 401199 - 202
231ILEILEVALVAL(chain B and ((resid 220 and (name N or name...BB403 - 411204 - 212
232GLYGLYMETMET(chain B and ((resid 220 and (name N or name...BB413 - 465214 - 266
233PROPROLYSLYS(chain B and ((resid 220 and (name N or name...BB469 - 475270 - 276
234CYSCYSSERSER(chain B and ((resid 220 and (name N or name...BB477 - 498278 - 299
335TYRTYRILEILE(chain C and ((resid 220 and (name N or name...CC220 - 23521 - 36
336LYSLYSILEILE(chain C and ((resid 220 and (name N or name...CC237 - 25338 - 54
337VALVALALAALA(chain C and ((resid 220 and (name N or name...CC255 - 25956 - 60
338GLNGLNALAALA(chain C and ((resid 220 and (name N or name...CC261 - 27462 - 75
339THRTHRTYRTYR(chain C and ((resid 220 and (name N or name...CC277 - 28378 - 84
340ILEILEGLUGLU(chain C and ((resid 220 and (name N or name...CC285 - 29586 - 96
341LYSLYSLEULEU(chain C and ((resid 220 and (name N or name...CC298 - 31399 - 114
342TYRTYRTYRTYR(chain C and ((resid 220 and (name N or name...CC315116
343THRTHRASNASN(chain C and ((resid 220 and (name N or name...CC317 - 342118 - 143
344VALVALPHEPHE(chain C and ((resid 220 and (name N or name...CC344 - 385145 - 186
345PROPROTYRTYR(chain C and ((resid 220 and (name N or name...CC387 - 394188 - 195
346GLYGLYLEULEU(chain C and ((resid 220 and (name N or name...CC398 - 401199 - 202
347ILEILEVALVAL(chain C and ((resid 220 and (name N or name...CC403 - 411204 - 212
348GLYGLYMETMET(chain C and ((resid 220 and (name N or name...CC413 - 465214 - 266
349PROPROLYSLYS(chain C and ((resid 220 and (name N or name...CC469 - 475270 - 276
350CYSCYSSERSER(chain C and ((resid 220 and (name N or name...CC477 - 498278 - 299
451TYRTYRILEILE(chain D and ((resid 220 and (name N or name...DD220 - 23521 - 36
454LYSLYSILEILE(chain D and ((resid 220 and (name N or name...DD237 - 25338 - 54
455VALVALALAALA(chain D and ((resid 220 and (name N or name...DD255 - 25956 - 60
456GLNGLNALAALA(chain D and ((resid 220 and (name N or name...DD261 - 27462 - 75
457THRTHRTYRTYR(chain D and ((resid 220 and (name N or name...DD277 - 28378 - 84
458ILEILEGLUGLU(chain D and ((resid 220 and (name N or name...DD285 - 29586 - 96
459LYSLYSLEULEU(chain D and ((resid 220 and (name N or name...DD298 - 31399 - 114
460TYRTYRTYRTYR(chain D and ((resid 220 and (name N or name...DD315116
461THRTHRASNASN(chain D and ((resid 220 and (name N or name...DD317 - 342118 - 143
462VALVALPHEPHE(chain D and ((resid 220 and (name N or name...DD344 - 385145 - 186
463PROPROTYRTYR(chain D and ((resid 220 and (name N or name...DD387 - 394188 - 195
464GLYGLYLEULEU(chain D and ((resid 220 and (name N or name...DD398 - 401199 - 202
465ILEILEVALVAL(chain D and ((resid 220 and (name N or name...DD403 - 411204 - 212
466GLYGLYMETMET(chain D and ((resid 220 and (name N or name...DD413 - 465214 - 266
467PROPROLYSLYS(chain D and ((resid 220 and (name N or name...DD469 - 475270 - 276
468CYSCYSSERSER(chain D and ((resid 220 and (name N or name...DD477 - 498278 - 299

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Components

#1: Protein
Protein kinase A regulatory subunit


Mass: 34476.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: PKAR, C3747_37g237 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86RB0
#2: Chemical
ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: PEG 3350 (15 to 26%), Calcium acetate (0,05 to 0,4M), drop size: 500nL protein (10 mg/ml with 250 uM guanosine) +500nL buffer. Protein Purification Buffer (Size Exclusion Chromatography): ...Details: PEG 3350 (15 to 26%), Calcium acetate (0,05 to 0,4M), drop size: 500nL protein (10 mg/ml with 250 uM guanosine) +500nL buffer. Protein Purification Buffer (Size Exclusion Chromatography): 10mM Hepes pH 7.0, 50 mM NaCl, 1% DMSO, 1mM DTT, *The 6His tag was cleaved for crystallisation

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→100 Å / Num. obs: 166708 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.0827459557 Å2 / Rrim(I) all: 0.134 / Net I/σ(I): 7.64
Reflection shellResolution: 2.08→2.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.08→59.8385267576 Å / SU ML: 0.460711273381 / Cross valid method: FREE R-VALUE / σ(F): 1.32759229407 / Phase error: 37.5656614622
RfactorNum. reflection% reflection
Rfree0.31914122542 8404 5.04290429043 %
Rwork0.259626840772 --
obs0.262630893136 166650 98.7181157961 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 96.5997128317 Å2
Refinement stepCycle: LAST / Resolution: 2.08→59.8385267576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8909 0 164 174 9247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01876826059269538
X-RAY DIFFRACTIONf_angle_d1.5421567932313020
X-RAY DIFFRACTIONf_chiral_restr0.07677100978261493
X-RAY DIFFRACTIONf_plane_restr0.0106188278161655
X-RAY DIFFRACTIONf_dihedral_angle_d17.39812231565718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0769-2.10050.3849646258742000.392214376273862X-RAY DIFFRACTION72.9525862069
2.1005-2.12530.4005510731723110.3516766302575377X-RAY DIFFRACTION99.5972684293
2.1253-2.15120.4202875372723010.3526979013535265X-RAY DIFFRACTION99.856476498
2.1512-2.17840.3924140448272820.3420695725455344X-RAY DIFFRACTION99.8402839397
2.1784-2.20710.3712584746182430.339438050485347X-RAY DIFFRACTION99.8392570102
2.2071-2.23730.3852427207872550.3306019692415445X-RAY DIFFRACTION99.4590821846
2.2373-2.26930.3663645907872590.3321300669615247X-RAY DIFFRACTION99.5120187963
2.2693-2.30310.4100168912752860.33713694135412X-RAY DIFFRACTION99.4415357766
2.3031-2.33910.4121882198353410.3412346265965193X-RAY DIFFRACTION99.7296810236
2.3391-2.37750.3810853277432820.3252558689635293X-RAY DIFFRACTION99.67816914
2.3775-2.41850.3743426224513480.3150171039915276X-RAY DIFFRACTION99.4694021931
2.4185-2.46250.3717187424372550.2995695649885338X-RAY DIFFRACTION99.2722754704
2.4625-2.50980.3805272040132830.3139311099845271X-RAY DIFFRACTION99.5162157319
2.5098-2.56110.3719645177992600.3097582634525349X-RAY DIFFRACTION99.7510225858
2.5611-2.61670.3304102152192530.3069023290955412X-RAY DIFFRACTION99.6306718255
2.6167-2.67760.3722942050882670.2919646096765297X-RAY DIFFRACTION99.659681175
2.6776-2.74460.3433939416183300.2777162575745307X-RAY DIFFRACTION99.7875730218
2.7446-2.81880.3639569183282570.2792558113565395X-RAY DIFFRACTION99.8939554613
2.8188-2.90170.3633738331623090.2709211060135257X-RAY DIFFRACTION99.8923187365
2.9017-2.99540.3326467495753240.2675019427835374X-RAY DIFFRACTION99.8073217726
2.9954-3.10240.3348601819162790.2687793974655300X-RAY DIFFRACTION99.8210771158
3.1024-3.22660.3530423680432800.2755074068795312X-RAY DIFFRACTION99.6081225508
3.2266-3.37350.342424572952870.2517169412235370X-RAY DIFFRACTION99.7355430183
3.3735-3.55130.2952930518832830.254214091235301X-RAY DIFFRACTION99.7855611151
3.5513-3.77380.3486860859812790.2605984739245339X-RAY DIFFRACTION99.5569732412
3.7738-4.06510.3307650999042470.2322228317155332X-RAY DIFFRACTION99.4828815977
4.0651-4.47410.2463840348722900.2111468679155281X-RAY DIFFRACTION99.4111349036
4.4741-5.12120.2482015517482610.2098684214225333X-RAY DIFFRACTION99.0965456156
5.1212-6.45090.2531166696522820.2207205160945289X-RAY DIFFRACTION99.4111349036
6.4509-59.86330.2728796041452700.2305563405975328X-RAY DIFFRACTION98.8172992056
Refinement TLS params.Method: refined / Origin x: 44.2055548748 Å / Origin y: -9.42040444533 Å / Origin z: 113.602336707 Å
111213212223313233
T0.471575595362 Å20.0296118576149 Å20.00206389151391 Å2-0.493123065004 Å2-0.0170951458482 Å2--0.605206373095 Å2
L-0.0521521140273 °20.0394352291189 °2-0.0678254451968 °2-0.0356847493883 °2-0.0445784364597 °2--0.463851063629 °2
S0.0224610802024 Å °0.0340178283859 Å °-0.0146629569591 Å °0.0053996177657 Å °0.0208901727465 Å °-0.00613945805963 Å °-0.0271465842257 Å °-0.043035766974 Å °-0.0541580830485 Å °
Refinement TLS groupSelection details: all

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