[English] 日本語
Yorodumi
- PDB-8xfd: Crystal structure of pyruvate kinase tetramer in complex with all... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xfd
TitleCrystal structure of pyruvate kinase tetramer in complex with allosteric activator, Mitapivat (MTPV, AG-348)
ComponentsIsoform L-type of Pyruvate kinase PKLR
KeywordsTRANSFERASE / pyruvate kinase / allosteric activator / Mitapivat / AG-348
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / phosphorylation / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSun, R. / Achour, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Crystals / Year: 2024
Title: High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/AG-348
Authors: Han, X. / Sandalova, T. / Zhang, C. / Mardinoglu, A. / Achour, A. / Sun, R.
History
DepositionDec 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform L-type of Pyruvate kinase PKLR
B: Isoform L-type of Pyruvate kinase PKLR
C: Isoform L-type of Pyruvate kinase PKLR
D: Isoform L-type of Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,61514
Polymers234,2574
Non-polymers2,35910
Water15,961886
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.930, 86.962, 91.554
Angle α, β, γ (deg.)76.780, 66.880, 80.220
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 24 through 134 or resid 140 through 199 or resid 202 through 551))
d_2ens_1(chain "B" and (resid 24 through 134 or resid 140 through 199 or resid 202 through 551))
d_3ens_1(chain "C" and (resid 24 through 134 or resid 140 through 551))
d_4ens_1(chain "D" and (resid 24 through 134 or resid 140 through 199 or resid 202 through 551))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNLEULEUAA24 - 13426 - 136
d_12SERSERGLYGLYAA140 - 199142 - 201
d_13GLYGLYILEILEAA202 - 540204 - 542
d_14MGMGMGMGAE601
d_15FBPFBPFBPFBPAF602
d_21GLNGLNLEULEUBB24 - 13426 - 136
d_22SERSERGLYGLYBB140 - 199142 - 201
d_23GLYGLYILEILEBB202 - 540204 - 542
d_24MGMGMGMGBG601
d_25FBPFBPFBPFBPBH602
d_31GLNGLNLEULEUCC24 - 13426 - 136
d_32SERSERILEILECC140 - 540142 - 542
d_33MGMGMGMGCJ601
d_34FBPFBPFBPFBPCK602
d_41GLNGLNLEULEUDD24 - 13426 - 136
d_42SERSERGLYGLYDD140 - 199142 - 201
d_43GLYGLYILEILEDD202 - 540204 - 542
d_44MGMGMGMGDL601
d_45FBPFBPFBPFBPDM602

NCS oper:
IDCodeMatrixVector
1given(-0.478615601668, -0.739065009867, 0.474035881585), (-0.761549487357, 0.0807177066945, -0.643060673756), (0.437000553942, -0.668780653889, -0.601467333143)12.7309671947, 31.9125162745, 38.9859807156
2given(-0.185761493484, 0.869907660122, 0.456895316675), (0.849742914247, -0.091260358623, 0.519238410204), (0.493385900919, 0.484698060451, -0.722245209724)6.97902378361, -29.3272866165, 40.8505531515
3given(-0.313329131558, -0.0601518815311, -0.94773762533), (-0.17004752609, -0.978307884475, 0.118311123928), (-0.934295827984, 0.198230760283, 0.296303681195)50.5208059769, 0.516456954915, 35.654183956

-
Components

#1: Protein
Isoform L-type of Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 58564.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-WV2 / mitapivat / N-{4-[4-(cyclopropylmethyl)piperazine-1-carbonyl]phenyl}quinoline-8-sulfonamide


Mass: 450.553 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C24H26N4O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 886 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Magnesium formate dihydrate, 20% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.1→84.32 Å / Num. obs: 131759 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.054 / Rrim(I) all: 0.076 / Χ2: 0.52 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 6456 / CC1/2: 0.963 / Rpim(I) all: 0.102 / Rrim(I) all: 0.145 / Χ2: 0.54 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→54.43 Å / SU ML: 0.2859 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.4174
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 6502 4.94 %
Rwork0.2317 125103 -
obs0.2333 131605 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15587 0 148 886 16621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008415990
X-RAY DIFFRACTIONf_angle_d121697
X-RAY DIFFRACTIONf_chiral_restr0.05682525
X-RAY DIFFRACTIONf_plane_restr0.022871
X-RAY DIFFRACTIONf_dihedral_angle_d23.112352
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.55226141995
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.93822645314
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.07654377599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.31352230.26464165X-RAY DIFFRACTION95.14
2.12-2.150.32362010.24824017X-RAY DIFFRACTION95.02
2.15-2.180.30362320.25314232X-RAY DIFFRACTION95.06
2.18-2.20.2971900.24484037X-RAY DIFFRACTION95.96
2.2-2.230.28252170.24674191X-RAY DIFFRACTION95.54
2.23-2.260.29052220.25124059X-RAY DIFFRACTION93.92
2.26-2.290.29622380.2534118X-RAY DIFFRACTION95.69
2.29-2.330.35611960.24644118X-RAY DIFFRACTION96.19
2.33-2.370.29652130.24634124X-RAY DIFFRACTION94.9
2.37-2.40.28872000.24214108X-RAY DIFFRACTION95.12
2.4-2.450.29922200.24354117X-RAY DIFFRACTION96.08
2.45-2.490.29492050.24684153X-RAY DIFFRACTION94.9
2.49-2.540.31272020.25334077X-RAY DIFFRACTION94.88
2.54-2.590.29531830.25384226X-RAY DIFFRACTION96.92
2.59-2.650.30662170.25254262X-RAY DIFFRACTION97.1
2.65-2.710.30132160.25624095X-RAY DIFFRACTION95.86
2.71-2.780.28242310.2514181X-RAY DIFFRACTION96.67
2.78-2.850.30042230.24654210X-RAY DIFFRACTION97.51
2.85-2.930.2562470.24354174X-RAY DIFFRACTION97.25
2.93-3.030.29272010.2424202X-RAY DIFFRACTION97.58
3.03-3.140.30842300.25044208X-RAY DIFFRACTION97.39
3.14-3.260.28222030.25154241X-RAY DIFFRACTION97.2
3.26-3.410.26462210.23934186X-RAY DIFFRACTION97.26
3.41-3.590.24732550.21814176X-RAY DIFFRACTION97.64
3.59-3.820.25772350.22424243X-RAY DIFFRACTION98.18
3.82-4.110.23221920.21514269X-RAY DIFFRACTION98.13
4.11-4.520.19712090.19994238X-RAY DIFFRACTION98.38
4.52-5.180.22332350.2024218X-RAY DIFFRACTION98.37
5.18-6.520.25892260.21944273X-RAY DIFFRACTION98.25
6.52-54.430.17852190.1854185X-RAY DIFFRACTION97.22
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)
10.2260249165280.094465424158-0.4438412245970.845692259008-0.1005987954192.13924728211-0.00309959610623-0.004308105057930.10223015413-0.0385557586392-0.0884023280237-0.160913088306-0.1335710333450.2901649801740.09067879581690.17087177267-0.0110490461993-0.02742107753680.3907877127510.1356278516920.24569360304412.59920.582-0.486
23.32614463319-0.879720795074-1.782217483534.141996492451.177688708066.044100328870.09998959694170.1997364243851.07934473101-0.6283680315130.0438739773002-0.430436149786-1.189204397250.650176863617-0.1525839773250.377788644631-0.143231425528-0.07177925593330.3638935450290.1065008969350.604745155314-21.32624.251-3.811
35.202347096841.06232489726-0.8522822111575.83860769879-0.008581521860384.79001377508-0.05393357235390.2104080343070.622882902147-0.030709381183-0.05379908159520.164641617953-0.4019612740740.05474314585850.09053752626320.151895563589-0.0157369039368-0.04652224486990.169112732365-0.02826036789530.231173527114-25.65916.3251.832
48.35593378678-1.32768764654-7.734016264973.969414211373.722595793978.81275626333-0.9703661908260.177324657407-0.830035502563-0.08635735611340.158208879437-0.252380584360.907958977656-0.1418902394460.8049432478960.293511412347-0.04384062930630.05379010888490.4421905754770.05285940558110.557485646537-13.6253.426-5.954
52.148360651482.23878331135-0.4571103215485.4191366914-2.375625685275.71623398034-0.1128310215130.635300580377-0.0258665483132-0.3721239874430.1204101817520.325349064270.219401487556-0.26288078181-0.0002182033064130.1486949562190.0487963348608-0.017780726240.255353323138-0.01119442107430.170023024878-1.2116.162-10.471
61.302219587060.0956074651740.0380617550461.921592692890.1724050320061.31471195341-0.009485367898110.107943514813-0.0055083483302-0.0940785493302-0.132098622653-0.1294432935110.01229538028620.2949011712650.1216286994110.1142757110250.009889568442459.42437411862E-50.2216345862230.04189508131230.09259230310014.60613.5676.873
78.91215668842-7.38768736829-9.729393850338.003232468868.250103836472.00303955192-0.4726781686210.284962038697-0.1546376607930.6797331338570.01140260102060.4208729195580.729009736804-0.3741767304990.4381785522920.300753700296-0.0922710920447-0.05779631214650.4060131920320.1109834142610.27842885716920.844-6.9759.268
83.35872318052-1.23981373710.6389885606242.017012867410.4640220713220.4514254882870.0636835942210.03385627452720.0546994479138-0.007117794252840.1465471095790.104527626994-0.0807349721617-0.456618010133-0.1892153560590.13223982474-0.0090228382624-0.01236792049610.2891912723620.07560235914150.13876574637825.8816.922-1.488
92.118411492220.1933257315430.5589023586757.86333654244-0.097135984331.78272703854-0.08784700612670.124119381160.187462461038-0.0288560694510.17004372418-0.191011355724-0.1320608477050.0952451137021-0.08086012190420.09714587931780.01514899041130.01105013826490.2277517937510.009990663081260.088765353404133.158.177-0.284
101.19204809087-0.50271575044-0.9635524402541.838315443431.044495072321.623094314860.0610013930224-0.02853031280860.08695710193020.117648492887-0.1237412095410.222309716622-0.2564323609490.03725614710460.06872892364810.300733931891-0.0213148216389-0.03021690967490.127177944363-0.005617631222550.122649756824-9.74223.22931.105
111.85276778898-1.216197259940.09253195498712.96109405303-1.222514010671.53007065732-0.195690620740.5341449345130.571070113719-0.312321371028-0.0864964697106-0.206806951757-0.4336340215840.05816520930260.2887865147410.615711958974-0.237920851487-0.1065197552090.4730998945140.06176767634430.3824397553194.37253.45818.478
124.94853628061-1.728146176240.0381512358042.92172644832-1.711109668142.403894510530.03163117156370.2543816782530.47017233118-0.554682273531-0.0441921124659-0.267118065033-0.2329697724680.1362882069150.000232068831410.726270088966-0.2414299417890.0382717837290.3652649682380.005055238099910.32672565735415.18451.40417.015
132.000426503810.505064744438-8.401522718390.663436393604-1.993011605242.000420226650.437642404317-0.494643592210.6213839641880.224952606921-0.177071652294-0.486913916228-0.5708759814710.303327340284-0.2593864574590.820605464435-0.3879595000020.1276657476610.7103975551020.01414383314240.530107349229.58147.04636.509
140.7971775607390.5996235609820.3731972833990.4534670107870.2772897432630.1726965551650.0917877344705-0.2185968081120.3276006302680.263091277653-0.0307716457548-0.0675270989689-0.2740363076030.109378644714-0.02431150241550.764183483558-0.555665959138-0.1173898516640.298146239588-0.12488774120.2168933412383.09640.1241.346
150.7811402089020.08184553071090.2620482618930.8049630325090.2517276838921.288093520670.0486338427752-0.09302276245440.04184577934510.214129621985-0.263684856677-0.172576454253-0.4060987101990.3181279107290.1754599685610.247613691129-0.143754027491-0.07937404668150.2531534151390.0500089691810.1761263312742.65925.58926.042
164.163042335510.9003313670444.993754429541.717813888833.107030518688.701983589610.1591653699130.143865948599-0.03948529312980.480401403944-0.155642737685-0.4738355959570.6167956238140.865617624133-0.002153467420710.301051968989-0.0584024139433-0.05113756348590.4308445715720.1451157227870.26146298062312.6277.32836.917
171.10028021876-0.287152369133-0.0629692274913.039846178040.09305180790922.52441929502-0.0342162635629-0.08684240801810.1195425864740.0722473255346-0.0816179435668-0.0467471056748-0.1944079038030.3454578849190.1101490614640.139815478763-0.0535522771414-0.04195560853830.1528199822670.02507720172550.119490674005-4.01813.71146.943
181.64648514812-0.2356221514150.7590214606792.101981913411.477392813515.00057206898-0.117200476994-0.0565074377577-0.06434431370550.0450726962336-0.1761091728350.3156464700010.1048395378350.1926281627940.2906280889570.143863410042-0.03924152091550.02900572083350.1213765742520.03245165752160.206907162348-8.8447.7948.764
190.7060916296210.27580237557-0.3055748966160.29597624869-0.1449571641330.542357993996-0.00939438308598-0.293292081753-0.0247673332470.008968045434580.3519692034980.08479937774380.0464303760638-0.24390778439-0.2533905039340.2222091813620.0437972617673-0.1012618817220.5438272621710.2613315389160.29811282169722.53-22.33457.047
203.036000880870.723710970978-1.8652894981.6065131073-1.277125422851.6262618708-0.09264517844730.176005208223-0.427935506763-0.242736686680.2841252791270.03496454273030.398710411667-0.131523318951-0.1804006780890.567721146548-0.05346913109-0.1550738477320.391113223591-0.07649572585710.87064906690232.545-54.76936.074
214.864878538931.48295149043-0.8745597039085.789327223750.3225024290122.1077893771-0.2181099904350.0676905486793-1.15735423101-0.4093789461770.5834920781750.2492162648540.857891976092-0.510565988215-0.3509713034140.741025900738-0.257904928827-0.1497912365850.5141961993810.1732887955840.73004518681520.799-55.61536.097
222.59824788871-1.0868381424-1.393838539951.59569055685-0.5532567346341.875655733030.1748036553370.205094478049-0.4659134541410.0401523376867-0.0680943952383-0.1425953790640.29499708359-0.309368806228-0.1000616537590.556800081137-0.257256950308-0.1922883902170.4793263869340.07427646808420.65683371303628.169-48.26133.783
233.349068301711.05534275058-5.025216034791.44236859907-2.432470824979.52803002328-0.3345903031270.343490643718-0.0929296017358-0.4296445494940.3751042386160.3340029082460.712258407143-0.834301147583-0.05970758775830.368815697869-0.155693188116-0.1625919594390.5873486975170.2714244653110.52628622087610.877-42.94545.656
240.2976076679650.02275604309780.05176487565440.2058639750030.5227762074651.32347191727-0.08040327243310.042698677052-0.0281017163716-0.0851276110180.09813526402490.2251645809320.15754273789-0.255170373443-0.04069111698670.206439848889-0.281083052613-0.02104667721970.608451109460.5382011541640.4377150488558.867-34.45249.783
250.5927010027551.268209254360.165878402044.70979305162.330045759541.995003883020.0472278766323-0.06764222856960.006122251727520.2500975044160.1588255921550.7800265681870.171981184771-0.808053103037-0.2244178049270.326182296741-0.0652607385815-0.02710167041390.9166233409590.5003920879720.7353845994850.333-33.54254.448
260.5271255292230.128366505593-0.2953743480180.4985860052480.3644347131880.8726703450990.0887437136892-0.03456891947180.0113519551327-0.1716592249130.4462767090770.101438542081-0.0116713921272-0.410335894636-0.2785887071340.199248002942-0.0694853411485-0.1359432718210.4965246064760.3449804358060.2566614438722.991-22.08344.651
271.83309350078-0.9072923897780.6424869561772.23527293204-0.7160951031920.597110951190.00903422218124-0.330965763591-0.06140750824430.0756870350594-0.178700598395-0.1906633917410.02165086868540.3026054771130.1640168932220.1964237195480.005756342824460.007449169512570.4971067658840.2134831248720.3235541773416.605-6.76657.281
281.39543458970.0128080173231-0.08150914994660.856585221091-0.1421276902641.085833592140.07586096194750.0599037077087-0.202841863578-0.2303540150810.1314424275240.07317931888840.367867647897-0.194344218376-0.192880089810.352811474816-0.0781260647662-0.03667932167960.1283543614730.01257130581760.18831249048945.839-22.30727.323
298.960380259771.77419618778-4.331289834196.78513033214-4.88050397794.612093508560.0360250711077-0.752680737479-0.797157057327-0.0648262207424-0.153286127754-0.1153544662390.6448227384310.5282588909420.1455614996970.3278638167090.0135850812708-0.007682936607870.41331261348-0.02401297443640.28091713066561.157-20.07362.832
301.60166561018-0.01225078854940.4861862621543.8270487139-0.04477312074064.30002445560.0503326331728-1.094932216660.1498557202020.626296659484-0.1374126287710.0143319278449-0.362185108074-0.155891367380.1023051707120.331632788813-0.0391303649912-0.01198703769320.655795116267-0.08185578728240.27378589253456.126-8.19462.686
316.694756208011.767684895520.3272793244329.283479981210.996977346226.448745141870.210903564361-0.5504505686830.3058356003730.611015204568-0.135655052682-0.474046835904-0.0839821972210.548252020161-0.06526961203720.138848695647-0.0486409468672-0.06254636461580.221607504644-0.06821859567440.26234301879265.774-8.78940.469
322.1567035541-2.67262895562-1.452832801945.067879033133.358924196413.961425973230.009152897144510.03141984642920.538366690779-0.199011344073-0.130363190773-0.261073043038-0.393231531550.1220345444390.04808005742780.22161936888-0.0305996020615-0.02810109855170.105521107488-0.05027949666170.2267308600260.029-6.30933.119
332.0712223396-0.127005810324-0.2931362715411.63834099487-0.01572290039821.64547064569-0.02987692604-0.05006023226790.0726114453059-0.05048818099380.1619215729090.0568001780560.142013912548-0.200985934808-0.1246734417280.128166183744-0.0279672052047-0.02477778585890.1196033275060.01230724024340.12015729371841.271-15.02137.048
346.567151496476.99802447143-4.269088690659.96022470019-0.09715242117881.999977753210.2578979920520.3049770586590.625008658762-0.2449511413910.2706302979490.8934154782-0.490882303987-0.701287252553-0.5117368313680.1850010816050.03702433741650.01333053493720.4633134341250.1302908831150.26181802068927.446-2.52325.064
353.409475807010.3517198824220.4694320543762.02430867753-1.097974256881.4978848136-0.009749573237150.0666630471756-0.231346977242-0.2122989245250.1149577715350.1200440617990.285342793457-0.213915258323-0.09033417799950.18610963127-0.0428304320289-0.04518593072560.1460127636490.005378749920660.12734483083742.539-9.82112.525
363.106323743860.262215190521-0.4571904843683.920156993970.5360019749572.555022581460.01547154987420.0172449735432-0.480529521267-0.2258268766380.07522977409190.2755471413370.562495718111-0.195767355338-0.04809383404620.252363407926-0.0236032675346-0.04407621966660.1477834888950.05669859032360.20262298273939.184-8.4946.026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:127 )A24 - 127
2X-RAY DIFFRACTION2( CHAIN A AND RESID 128:146 )A128 - 146
3X-RAY DIFFRACTION3( CHAIN A AND RESID 147:224 )A147 - 224
4X-RAY DIFFRACTION4( CHAIN A AND RESID 225:233 )A225 - 233
5X-RAY DIFFRACTION5( CHAIN A AND RESID 234:265 )A234 - 265
6X-RAY DIFFRACTION6( CHAIN A AND RESID 266:408 )A266 - 408
7X-RAY DIFFRACTION7( CHAIN A AND RESID 409:420 )A409 - 420
8X-RAY DIFFRACTION8( CHAIN A AND RESID 421:499 )A421 - 499
9X-RAY DIFFRACTION9( CHAIN A AND RESID 500:540 )A500 - 540
10X-RAY DIFFRACTION10( CHAIN B AND RESID 24:123 )B24 - 123
11X-RAY DIFFRACTION11( CHAIN B AND RESID 124:145 )B124 - 145
12X-RAY DIFFRACTION12( CHAIN B AND RESID 146:227 )B146 - 227
13X-RAY DIFFRACTION13( CHAIN B AND RESID 228:233 )B228 - 233
14X-RAY DIFFRACTION14( CHAIN B AND RESID 234:272 )B234 - 272
15X-RAY DIFFRACTION15( CHAIN B AND RESID 273:401 )B273 - 401
16X-RAY DIFFRACTION16( CHAIN B AND RESID 402:415 )B402 - 415
17X-RAY DIFFRACTION17( CHAIN B AND RESID 416:498 )B416 - 498
18X-RAY DIFFRACTION18( CHAIN B AND RESID 499:540 )B499 - 540
19X-RAY DIFFRACTION19( CHAIN C AND RESID 24:134 )C24 - 134
20X-RAY DIFFRACTION20( CHAIN C AND RESID 139:154 )C139 - 154
21X-RAY DIFFRACTION21( CHAIN C AND RESID 155:181 )C155 - 181
22X-RAY DIFFRACTION22( CHAIN C AND RESID 182:221 )C182 - 221
23X-RAY DIFFRACTION23( CHAIN C AND RESID 222:240 )C222 - 240
24X-RAY DIFFRACTION24( CHAIN C AND RESID 241:265 )C241 - 265
25X-RAY DIFFRACTION25( CHAIN C AND RESID 266:274 )C266 - 274
26X-RAY DIFFRACTION26( CHAIN C AND RESID 275:409 )C275 - 409
27X-RAY DIFFRACTION27( CHAIN C AND RESID 410:540 )C410 - 540
28X-RAY DIFFRACTION28( CHAIN D AND RESID 24:128 )D24 - 128
29X-RAY DIFFRACTION29( CHAIN D AND RESID 129:145 )D129 - 145
30X-RAY DIFFRACTION30( CHAIN D AND RESID 146:229 )D146 - 229
31X-RAY DIFFRACTION31( CHAIN D AND RESID 230:238 )D230 - 238
32X-RAY DIFFRACTION32( CHAIN D AND RESID 239:273 )D239 - 273
33X-RAY DIFFRACTION33( CHAIN D AND RESID 274:402 )D274 - 402
34X-RAY DIFFRACTION34( CHAIN D AND RESID 403:409 )D403 - 409
35X-RAY DIFFRACTION35( CHAIN D AND RESID 410:511 )D410 - 511
36X-RAY DIFFRACTION36( CHAIN D AND RESID 512:540 )D512 - 540

+
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