[English] 日本語
Yorodumi
- PDB-8aj8: Structure of p110 gamma bound to the p84 regulatory subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aj8
TitleStructure of p110 gamma bound to the p84 regulatory subunit
Components
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
  • Phosphoinositide 3-kinase regulatory subunit 6
KeywordsSIGNALING PROTEIN / PI3K / PIK3CG / PIK3R6 / phosphoinositide 3-kinase / p110 / p84
Function / homology
Function and homology information


G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol 3-kinase complex, class IA ...G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / positive regulation of T cell differentiation / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / immune system process / positive regulation of MAP kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / endocytosis / positive regulation of angiogenesis / chemotaxis / cell migration / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / G protein-coupled receptor signaling pathway / inflammatory response / protein serine kinase activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Phosphoinositide 3-kinase regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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 regulatory subunit 5/6 / Phosphoinositide 3-kinase gamma adapter protein p101 subunit / PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / Phosphoinositide 3-kinase regulatory subunit 6
Similarity search - Component
Biological speciesSus scrofa (pig)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.5 Å
AuthorsBurke, J.E. / Williams, R.L. / Zhang, X.
Funding support United Kingdom, Canada, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
Canadian Institutes of Health Research (CIHR)168998 Canada
CitationJournal: Cell Rep / Year: 2023
Title: Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs.
Authors: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / ...Authors: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / Calvin K Yip / Roger L Williams / Scott D Hansen / John E Burke /
Abstract: Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled ...Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
B: Phosphoinositide 3-kinase regulatory subunit 6
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
D: Phosphoinositide 3-kinase regulatory subunit 6
E: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
F: Phosphoinositide 3-kinase regulatory subunit 6
G: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
H: Phosphoinositide 3-kinase regulatory subunit 6


Theoretical massNumber of molelcules
Total (without water)846,4038
Polymers846,4038
Non-polymers00
Water00
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
B: Phosphoinositide 3-kinase regulatory subunit 6


Theoretical massNumber of molelcules
Total (without water)211,6012
Polymers211,6012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
D: Phosphoinositide 3-kinase regulatory subunit 6


Theoretical massNumber of molelcules
Total (without water)211,6012
Polymers211,6012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
F: Phosphoinositide 3-kinase regulatory subunit 6


Theoretical massNumber of molelcules
Total (without water)211,6012
Polymers211,6012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
H: Phosphoinositide 3-kinase regulatory subunit 6


Theoretical massNumber of molelcules
Total (without water)211,6012
Polymers211,6012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)322.347, 166.598, 255.794
Angle α, β, γ (deg.)90.000, 114.024, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "E"
d_4ens_1chain "G"
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULYSA1 - 995
d_21ens_1GLULYSC1 - 995
d_31ens_1GLULYSE1 - 995
d_41ens_1GLULYSG1 - 995
d_11ens_2SERGLNB1 - 558
d_21ens_2SERGLND1 - 558
d_31ens_2SERGLNF1 - 558
d_41ens_2SERGLNH1 - 558

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999994641788, -0.00202890867663, 0.00256903197895), (0.00201541818863, 0.999984224711, 0.00524293995871), (-0.0025796288981, -0.00523773419215, 0.999982955682)4.95692737026, 81.9467022275, 20.2094895081
2given(-0.995672539242, 0.0197712490206, -0.0908035919576), (-0.00743073228929, -0.990915633154, -0.134279530047), (-0.0926335728442, -0.133023703467, 0.986774399495)-0.673712310169, 44.0792667864, 5.91278487541
3given(-0.993187016113, 0.0291504406243, -0.112826427915), (-0.0117837846656, -0.98836712914, -0.151629681969), (-0.11593400469, -0.149267109058, 0.98197690233)5.49955990194, -39.9096304752, 25.6942608986
4given(0.999135295165, 0.028569246637, 0.0302069545246), (-0.0280296683355, 0.999442522789, -0.0181378426221), (-0.0307082993351, 0.0172754678251, 0.999379086515)4.70405349802, 83.9980144973, 20.7170008013
5given(-0.996118787943, 0.0285196090499, -0.0832705962959), (-0.021185572691, -0.995924583074, -0.0876663922966), (-0.0854314451335, -0.085562005167, 0.992663392825)-0.00433677885863, 44.4443405396, 5.31732223578
6given(-0.996163452997, 0.00828033799606, -0.0871195208647), (0.00345975470992, -0.991008858394, -0.13375153338), (-0.0874437248199, -0.133539801508, 0.98717815839)5.03388012802, -40.8766576239, 23.6002091712

-
Components

#1: Protein
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / ...PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit gamma / PtdIns-3-kinase subunit p110-gamma / p110gamma / Phosphoinositide-3-kinase catalytic gamma polypeptide / Serine/threonine protein kinase PIK3CG / p120-PI3K


Mass: 126830.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PIK3CG / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O02697, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Protein
Phosphoinositide 3-kinase regulatory subunit 6 / Phosphoinositide 3-kinase gamma adapter protein of 87 kDa / p84 PI3K adapter protein / p84 PIKAP / ...Phosphoinositide 3-kinase gamma adapter protein of 87 kDa / p84 PI3K adapter protein / p84 PIKAP / p87 PI3K adapter protein / p87PIKAP


Mass: 84769.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pik3r6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3U6Q4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL- ...Details: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 0.08 M buffer 2 pH7.5 (0.5 M HEPES, 0.5 M MOPS), 0.4 M Na/K phosphate pH 6.3.
PH range: 6.3-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 8.5→90.3 Å / Num. obs: 10835 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 484.61 Å2 / CC1/2: 0.99 / CC star: 0.129 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.066 / Rrim(I) all: 0.129 / Rsym value: 0.122 / Net I/σ(I): 6.8
Reflection shellResolution: 8.5→8.89 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1187 / CC1/2: 0.9 / Rpim(I) all: 0.228 / Rrim(I) all: 0.463 / Rsym value: 0.39

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLM7.0.3data reduction
SCALA6data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MEZ

7mez


Resolution: 8.5→90.29 Å / SU ML: 1.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.6969
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3399 1084 10 %
Rwork0.2795 9751 -
obs0.2857 10835 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 545.97 Å2
Refinement stepCycle: LAST / Resolution: 8.5→90.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50008 0 0 0 50008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003851076
X-RAY DIFFRACTIONf_angle_d0.634969220
X-RAY DIFFRACTIONf_chiral_restr0.04227916
X-RAY DIFFRACTIONf_plane_restr0.00588768
X-RAY DIFFRACTIONf_dihedral_angle_d10.683219152
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.0813187226868
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.100133135077
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.0957579923772
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.117716413945
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.11339534884
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.114664888476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
8.5-8.890.36041310.31311187X-RAY DIFFRACTION96.84
8.89-9.350.34031370.29011219X-RAY DIFFRACTION98.47
9.35-9.940.32151350.25341219X-RAY DIFFRACTION98.47
9.94-10.70.29741350.24681220X-RAY DIFFRACTION98.26
10.71-11.780.29461350.24221210X-RAY DIFFRACTION97.82
11.78-13.480.30611380.25781229X-RAY DIFFRACTION97.57
13.49-16.960.3381370.28241223X-RAY DIFFRACTION97.42
16.97-90.290.41221360.33281244X-RAY DIFFRACTION96.17
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)
13.158314941721.60281079137-0.385818351421.81086363436-2.349170337321.97313882658-0.1470089449590.3488900183680.7439198286580.03391067580610.200744815260.5454738067410.6331956309140.2851671821123.61670256035E-55.487047510920.1536636441710.2074934230914.53250518447-0.7086636248695.2698184690834.7056773346-6.1258708123466.7501442754
27.632011208572.016292920972.06635000222-0.5214703806811.063763490194.81273155612-1.946862899940.604667810491-1.664029613841.1335631331.73133979717-0.418142934013-0.521476147788-1.245668431930.0001600902645315.481933509010.755549716971-0.4282469000965.171228866390.3063491168566.0950748547554.9824969793-1.8010661550210.2018361738
32.668602353141.50813747851-0.5412310936321.19435535807-1.748624408611.616193830760.6904488850090.714773598566-0.376719176843-0.205653489199-0.396790645342-0.4455570283620.813218715777-0.9165564785242.78189583259E-55.48761175133-0.118757014248-0.09927440167675.02731177473-0.8077063710865.5682091544839.846252266576.240927313686.9010091646
46.003320728440.05386310180461.25119651334-1.987791826391.35260838372-0.158240763188-0.04396934530822.0026699185-0.582292970499-0.2696173799230.7187362968350.517862908715-0.572111566039-1.044466991610.0004994201262836.491066114680.5100124839110.02969468869447.454925581360.01412646806864.9326658587359.895509794180.471600589829.1931047138
52.892999076091.606304250131.835945996721.05017020709-1.191203825153.280477351550.283444203269-1.15019400516-0.1665365018780.0660982861194-0.121549892418-1.11769598214-0.6424030335650.392126281823.10978590633E-55.039427144661.025692819930.1959033619775.761374998060.107503824075.60412637952-41.411501225940.928449800169.3800204751
610.92111163862.406093454461.912844671846.00880914535-0.8562485180692.94663628684-1.437819461410.8853336069360.0819994724615-1.153875061951.071636980753.17897624874-0.7520343352960.2523556028880.0003420437130345.481605453140.436469246941.137400665364.62132747739-0.09935564917275.7296211477-55.673986636344.17886515810.9010826558
71.846981305773.198766771490.9445829798710.275328374397-0.131879935093-0.3339522310750.121014661217-1.05661760363-0.416545070176-0.2886026064160.0404224172035-1.05235034987-0.254848840038-0.5401186534861.25801398017E-55.362017429621.2816012975-0.589424779787.12838019310.1571267470856.7348312012-36.6794630081-44.385170753988.1320885219
86.18088811582-0.6077974206251.81491567582-2.26344984858-1.44671110141.244535218150.187602976182-0.3962615791670.981035866594-0.560616440259-0.258706410144-0.536543332262-0.09524966840941.281534591510.0001096990406366.14259399173-0.00144363924162-0.3440754485266.54881684473-0.1483609542385.11713790748-50.6410069962-40.265844232929.1037506669
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 36 through 1086)AA36 - 10781 - 995
22(chain 'B' and resid 3 through 756)BB3 - 7561 - 558
33(chain 'C' and resid 36 through 1086)CC36 - 10781 - 995
44(chain 'D' and resid 3 through 756)DD3 - 7561 - 558
55(chain 'E' and resid 36 through 1086)EE36 - 10781 - 995
66(chain 'F' and resid 3 through 756)FF3 - 7561 - 558
77(chain 'G' and resid 36 through 1086)GG36 - 10781 - 995
88(chain 'H' and resid 3 through 756)HH3 - 7561 - 558

+
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