[English] 日本語
Yorodumi
- PDB-8v8j: PI3Ka H1047R co-crystal structure with inhibitors in two cryptic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v8j
TitlePI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 5).
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsSIGNALING PROTEIN / H1047R / PI3K / PI3Ka
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / cis-Golgi network / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / RHOF GTPase cycle / kinase activator activity / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / relaxation of cardiac muscle / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte migration / positive regulation of filopodium assembly / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / phosphatidylinositol 3-kinase / growth hormone receptor signaling pathway / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / negative regulation of macroautophagy / 1-phosphatidylinositol-3-kinase activity / RHOB GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / protein kinase activator activity / response to dexamethasone / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / negative regulation of anoikis / RHOG GTPase cycle / intercalated disc / T cell differentiation / RET signaling / regulation of multicellular organism growth / extrinsic apoptotic signaling pathway via death domain receptors / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis
Similarity search - Function
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Rho GTPase activation protein / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / : / : / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsGunn, R.J. / Lawson, J.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein.
Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / ...Authors: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jones, B. / Kuehler, J. / Lawson, J.D. / Nguyen, N. / Parker, C. / Pearson, K.E. / Rahbaek, L. / Saechao, B. / Wang, X. / Waters, A. / Waters, L. / Watkins, A.H. / Olson, P. / Smith, C.R. / Christensen, J.G. / Marx, M.A.
History
DepositionDec 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,57810
Polymers316,9554
Non-polymers2,6236
Water0
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7895
Polymers158,4772
Non-polymers1,3123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-14 kcal/mol
Surface area59960 Å2
MethodPISA
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7895
Polymers158,4772
Non-polymers1,3123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-17 kcal/mol
Surface area59710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.940, 158.480, 121.600
Angle α, β, γ (deg.)90.000, 112.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 102 or resid 104...
d_2ens_1(chain "C" and (resid 2 through 102 or resid 104...
d_1ens_2(chain "B" and (resid 326 through 329 or resid 331...
d_2ens_2(chain "D" and (resid 326 through 329 or resid 331...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROILEILEAA2 - 1026 - 106
d_12ens_1PROPROARGARGAA104 - 309108 - 313
d_13ens_1THRTHRASPASPAA322 - 350326 - 354
d_14ens_1ILEILEASNASNAA354 - 497358 - 501
d_15ens_1ARGARGARGARGAA524528
d_16ens_1ASNASNPROPROAA526 - 609530 - 613
d_17ens_1VALVALGLNGLNAA611 - 728615 - 732
d_18ens_1VALVALMETMETAA730 - 739734 - 743
d_19ens_1ARGARGASPASPAA741 - 883745 - 887
d_110ens_1ASNASNGLYGLYAA885 - 887889 - 891
d_111ens_1ILEILELYSLYSAA889 - 941893 - 945
d_112ens_1GLUGLUGLUGLUAA950954
d_113ens_1VALVALTHRTHRAA952 - 974956 - 978
d_114ens_1GLUGLULYSLYSAA976 - 1054980 - 1058
d_115ens_1ASPASPGLNGLNAA1056 - 10641060 - 1068
d_116ens_1R07R07R07R07AE1101
d_21ens_1PROPROILEILECC2 - 1026 - 106
d_22ens_1PROPROARGARGCC104 - 309108 - 313
d_23ens_1THRTHRASPASPCC322 - 350326 - 354
d_24ens_1ILEILEASNASNCC354 - 497358 - 501
d_25ens_1ARGARGARGARGCC524528
d_26ens_1ASNASNPROPROCC526 - 609530 - 613
d_27ens_1VALVALGLNGLNCC611 - 728615 - 732
d_28ens_1VALVALMETMETCC730 - 739734 - 743
d_29ens_1ARGARGASPASPCC741 - 883745 - 887
d_210ens_1ASNASNGLYGLYCC885 - 887889 - 891
d_211ens_1ILEILELYSLYSCC889 - 941893 - 945
d_212ens_1GLUGLUGLUGLUCC950954
d_213ens_1VALVALTHRTHRCC952 - 974956 - 978
d_214ens_1GLUGLULYSLYSCC976 - 1054980 - 1058
d_215ens_1ASPASPGLNGLNCC1056 - 10641060 - 1068
d_216ens_1R07R07R07R07CF1101
d_11ens_2METMETGLNGLNBB326 - 3295 - 8
d_12ens_2ALAALAALAALABB33110
d_13ens_2TRPTRPGLNGLNBB333 - 43312 - 112
d_14ens_2VALVALLEULEUBB445 - 449124 - 128
d_15ens_2GLUGLUSERSERBB451 - 505130 - 184
d_16ens_2GLUGLUILEILEBB507 - 509186 - 188
d_17ens_2LYSLYSARGARGBB511 - 514190 - 193
d_18ens_2GLYGLYILEILEBB516 - 571195 - 250
d_19ens_2LEULEUARGARGBB573 - 574252 - 253
d_110ens_2THRTHRTHRTHRBB576255
d_21ens_2METMETGLNGLNDD326 - 3295 - 8
d_22ens_2ALAALAALAALADD33110
d_23ens_2TRPTRPGLNGLNDD333 - 43312 - 112
d_24ens_2VALVALLEULEUDD445 - 449124 - 128
d_25ens_2GLUGLUSERSERDD451 - 505130 - 184
d_26ens_2GLUGLUILEILEDD507 - 509186 - 188
d_27ens_2LYSLYSARGARGDD511 - 514190 - 193
d_28ens_2GLYGLYILEILEDD516 - 571195 - 250
d_29ens_2LEULEUARGARGDD573 - 574252 - 253
d_210ens_2THRTHRTHRTHRDD576255

NCS ensembles :
ID
ens_1
ens_2

-
Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform


Mass: 124810.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42336
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 33666.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27986
#3: Chemical ChemComp-YO4 / 2-({(1R)-1-[2-(4,4-dimethylpiperidin-1-yl)-3,6-dimethyl-4-oxo-4H-1-benzopyran-8-yl]ethyl}amino)benzoic acid


Mass: 448.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-YOR / N-{(3S)-3-(2-methylphenyl)-6-[(oxetan-3-yl)amino]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}-1-benzothiophene-3-carboxamide


Mass: 469.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23N3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-YNZ / (2S)-N~1~-[(4P)-2-tert-butyl-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]pyrrolidine-1,2-dicarboxamide


Mass: 393.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N5O2S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.4M Sodium Formate, 0.1 M Sodium Citrate, pH 5.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.35→43.471 Å / Num. obs: 59463 / % possible obs: 99.86 % / Redundancy: 6.2 % / Biso Wilson estimate: 89.42 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 6.5
Reflection shellResolution: 3.35→3.37 Å / Num. unique obs: 59512 / Rpim(I) all: 0.36

-
Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→43.47 Å / SU ML: 0.4725 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 2937 4.94 %RANDOM
Rwork0.2091 56526 --
obs0.2112 59463 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.69 Å2
Refinement stepCycle: LAST / Resolution: 3.35→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20712 0 186 0 20898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002421358
X-RAY DIFFRACTIONf_angle_d0.616828826
X-RAY DIFFRACTIONf_chiral_restr0.0423093
X-RAY DIFFRACTIONf_plane_restr0.00353680
X-RAY DIFFRACTIONf_dihedral_angle_d14.2248163
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.82409044106
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.36642378282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40.40441420.33842707X-RAY DIFFRACTION99.96
3.4-3.460.35981320.30172695X-RAY DIFFRACTION99.96
3.46-3.530.38421540.27852656X-RAY DIFFRACTION99.96
3.53-3.590.29431470.25092667X-RAY DIFFRACTION100
3.59-3.670.28381220.23352713X-RAY DIFFRACTION99.96
3.67-3.750.28041530.22162656X-RAY DIFFRACTION99.96
3.75-3.830.26711310.22232704X-RAY DIFFRACTION99.89
3.83-3.930.29831400.2222684X-RAY DIFFRACTION100
3.93-4.040.25921380.21822654X-RAY DIFFRACTION100
4.04-4.160.25321310.22132705X-RAY DIFFRACTION100
4.16-4.290.24521480.19522681X-RAY DIFFRACTION99.96
4.29-4.440.19571410.1862698X-RAY DIFFRACTION100
4.44-4.620.22221480.18232660X-RAY DIFFRACTION99.93
4.62-4.830.2181350.18492718X-RAY DIFFRACTION99.96
4.83-5.080.2271420.18622689X-RAY DIFFRACTION100
5.08-5.40.23911370.19392688X-RAY DIFFRACTION100
5.4-5.820.26391300.21672715X-RAY DIFFRACTION99.96
5.82-6.40.3011470.23472696X-RAY DIFFRACTION100
6.4-7.330.2141320.22772717X-RAY DIFFRACTION100
7.33-9.210.23881460.18822715X-RAY DIFFRACTION99.93
9.21-43.470.21581410.17512708X-RAY DIFFRACTION97.74
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)
11.64658301956-1.089758117830.09511486596082.55266348576-0.8872235223781.581204405650.08254549254790.0158587697934-0.0382976296769-0.165661458787-0.03515290230150.1614668538140.02741774609870.0740675382506-0.02513370143170.685452796887-0.0462375568562-0.003601185662240.589116579956-0.02656076516460.65666201885133.041137949830.144044992913.4589764535
20.623171938034-0.2773283293810.02189066795421.93196741614-0.8806845891733.86618759578-0.0378797510673-0.189143627491-0.07297901498440.124367385993-0.02462086452550.1863738583630.07238670466090.119859476291-0.05246236344880.532803911926-0.08078710390850.03842893027610.619112150457-0.01563279748310.60977258739335.2179936506-5.1171715537239.6678258092
31.0698803013-0.195379269821-0.07287482146051.958763171530.2159005835262.480897752750.1114395264190.295756338916-0.337233460633-0.747539424043-0.01791890588440.5007617578680.101565434589-0.29122095219-0.0637215537641.039889978230.0064510581981-0.3056223262690.754894779938-0.1621560704860.87857711462726.5711486405-16.4888608945-2.7974894984
41.56894555489-0.220141431811-0.09032730794791.595456017750.02542958622111.235928285470.0607385814898-0.0864567516521-0.146648053326-0.129550467441-0.0667084453339-0.1684816561020.2017269187380.2459254299690.02523915853080.5974248297410.03231054278870.01682696980.575433414218-0.003622291843260.4625063752755.2889714345-6.6377179256718.6620142796
51.639535250820.4621022886492.472606244910.1448102763590.7395789469293.75942794362-0.5789133931350.731707433788-0.13050784624-0.00443813432347-0.04129456971020.543947875434-0.531125504719-0.272210898810.1373294669262.666606363010.1927957555220.1590677033372.241966366310.03083329392312.1002059532542.8296215018-38.1324975655-13.1791603574
60.975004784814-1.24693008986-0.6927690000042.435223790990.9107136447710.3058820405240.3390389502070.202393158471-0.198500313712-0.982695733642-0.265095657487-0.0137777419837-0.2427732191650.103642449876-0.0986613895671.262183550490.1313207624630.01828772750430.959293393193-0.08663502287160.91825160800641.479359861315.4303422029-9.02675501227
72.67799289754-0.644274833660.02619993789811.92546100858-0.00234972427722.76202227073-0.04914164547870.138588715246-0.65654102779-0.1755445400870.120955002171-0.4652459987260.3634792531510.4839471779190.07730515901180.5105792573950.1054903025610.04361855321540.684535356097-0.05869844261581.1527252810763.3042774122-34.897657553189.5947927167
81.08971818417-0.0301599096948-0.3866321639861.422286373660.9880971354380.809937387765-0.0601582039176-0.223523185236-0.2265110914380.04645307174960.13827080098-0.749474427807-0.00813310963770.504527649193-0.2289428699230.507877989422-0.0232120933041-0.07268627880440.97672492117-0.07752067357140.9398786254668.1178244228-14.743264977696.0357915236
92.50491146847-0.217176488968-1.509974933642.128232065110.4061897726332.522277722680.0798359236669-0.3378046095750.1646052842030.0627429281518-0.004583322114410.0346493378775-0.428140260554-0.0227534306726-0.1242877340030.7285114694610.02763096651690.00681414477950.682061957207-0.07010152518150.62287417587833.51061680396.70970109493110.1128824
101.953561343520.168998478942-0.2319728444341.35542310912-0.1215085017530.0382668470739-0.524964652818-0.16979716378-0.59555470158-0.3446706839770.0946182340176-0.7753227503840.006416272328720.4612043749780.2404802749260.846799372295-0.1641434812850.1135197549911.0087433045-0.0626109186841.0219423032872.94157503023.1498748787292.6689928254
111.40683743216-0.315738970667-0.4659921714352.29887217493-0.2347930786141.18759576663-0.008992352203840.2155626302540.0161099748919-1.37957958825-0.128714190024-1.2149584928-0.3892527659970.6671408069070.1384965547731.32589681172-0.4997066893010.6079061317011.47001181149-0.212998979531.6562699644884.167546287511.299774753875.0747372187
121.390704683670.3933331119090.147613065482.134479314460.1430424463121.32633660591-0.07965658357960.03524689867650.192430148367-0.1277249817060.122011175569-0.459993221463-0.3863325217630.388806220378-0.04507753038590.577575968321-0.1746584259820.087904083880.729160986475-0.05020617976520.68226427551158.93182620987.8126085502489.1935479401
132.46200167067-0.2252565965590.4669933572772.1673447760.1945085051412.19854452126-0.06082880451240.2392225364110.22659116-0.2288181778830.0146252429142-0.0130748625889-0.73712322748-0.173443823071-0.004822949558450.9172235681730.02631108385340.07709881412610.6506841647420.08609996422860.57551725010433.695440976312.474643788376.007076293
140.8277186608370.496418319510.5158624527021.878722987420.5631676390451.81277896321-0.09288636923870.3579684353640.443497268776-0.477230050280.008216058957480.0170450572905-0.8455214067520.05657488386380.04009963679461.18987052316-0.1477968838760.1644215373020.7501395569710.09604592032020.86641339488745.977166962520.659563337370.6678909547
150.486379915490.1173027045870.05585467097560.127438080537-0.2626228637750.6998563310840.3462385091710.290267480861-0.182959934976-0.691875426083-0.09339047356740.104196364772-1.681029094720.1250541007460.08177498605792.996941101470.3328215526440.3245200166212.46476288260.1533047567782.5379586951671.23755711338.694936702665.5661915613
160.271644171190.317292761522-0.07725329265841.082987920820.3266697419280.517000141932-0.01282663463690.15638673369-0.175058205906-0.80776943374-0.187702176242-0.5711179435140.01876233394730.4144198403790.2542596173730.912140790554-0.04082621468750.2372717492221.37943291676-0.1727497432721.2391525064172.8974640104-13.965880948568.6824356237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 121 )AA2 - 1211 - 120
22chain 'A' and (resid 122 through 296 )AA122 - 296121 - 295
33chain 'A' and (resid 297 through 647 )AA297 - 647296 - 603
44chain 'A' and (resid 648 through 1064 )AA648 - 1064604 - 1017
55chain 'B' and (resid 326 through 428 )BC326 - 4281 - 89
66chain 'B' and (resid 429 through 587 )BC429 - 58790 - 239
77chain 'C' and (resid 2 through 73 )CD2 - 731 - 72
88chain 'C' and (resid 74 through 154 )CD74 - 15473 - 153
99chain 'C' and (resid 155 through 282 )CD155 - 282154 - 281
1010chain 'C' and (resid 283 through 354 )CD283 - 354282 - 340
1111chain 'C' and (resid 355 through 477 )CD355 - 477341 - 458
1212chain 'C' and (resid 478 through 807 )CD478 - 807459 - 763
1313chain 'C' and (resid 808 through 993 )CD808 - 993764 - 942
1414chain 'C' and (resid 994 through 1064 )CD994 - 1064943 - 1013
1515chain 'D' and (resid 326 through 428 )DF326 - 4281 - 89
1616chain 'D' and (resid 429 through 587 )DF429 - 58790 - 239

+
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://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