[English] 日本語
Yorodumi
- PDB-8k7l: Crystal structure of human lysosomal alpha-galactosidase A in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k7l
TitleCrystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-(aminomethyl)-5-(hydroxymethyl)-1-methylpyrrolidine-3,4-diol
ComponentsAlpha-galactosidase A
KeywordsHYDROLASE / alpha-galactosidase / glycosidase / iminosugar
Function / homology
Function and homology information


glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Glycosyl hydrolase, all-beta / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Alpha-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H.Y. / Huang, K.F. / Ko, T.P. / Cheng, W.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Jacs Au / Year: 2024
Title: Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase.
Authors: Li, H.Y. / Lin, H.Y. / Chang, S.K. / Chiu, Y.T. / Hou, C.C. / Ko, T.P. / Huang, K.F. / Niu, D.M. / Cheng, W.C.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-galactosidase A
B: Alpha-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,50316
Polymers90,7892
Non-polymers3,71314
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-38 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.104, 90.104, 215.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 32 through 61 or resid 63...
d_2ens_1(chain "B" and (resid 32 through 61 or resid 63...

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_11LEULEUASPASPAA32 - 611 - 30
d_12CYSCYSLYSLYSAA63 - 23732 - 206
d_13ILEILELYSLYSAA239 - 240208 - 209
d_14ILEILELEULEUAA242 - 344211 - 313
d_15GLYGLYMETMETAA346 - 421315 - 390
d_16NAGNAGNAGNAGAG501
d_17NAGNAGNAGNAGCC1
d_18NAGNAGNAGNAGCC2
d_19NAGNAGNAGNAGDD2
d_110VO0VO0VO0VO0AH502
d_21LEULEUASPASPBB32 - 611 - 30
d_22CYSCYSLYSLYSBB63 - 23732 - 206
d_23ILEILELYSLYSBB239 - 240208 - 209
d_24ILEILELEULEUBB242 - 344211 - 313
d_25GLYGLYMETMETBB346 - 421315 - 390
d_26NAGNAGNAGNAGEE1
d_27NAGNAGNAGNAGEE2
d_28NAGNAGNAGNAGFF1
d_29NAGNAGNAGNAGBL501
d_210VO0VO0VO0VO0BM502

NCS oper: (Code: givenMatrix: (-0.96717397765, -0.251125409416, -0.0388654821474), (-0.246142440642, 0.88779720381, 0.388883046457), (-0.0631537478812, 0.385684007515, -0.920466974136)Vector: 87. ...NCS oper: (Code: given
Matrix: (-0.96717397765, -0.251125409416, -0.0388654821474), (-0.246142440642, 0.88779720381, 0.388883046457), (-0.0631537478812, 0.385684007515, -0.920466974136)
Vector: 87.8043009713, 14.6690348414, -15.3559585035)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alpha-galactosidase A / Alpha-D-galactosidase A / Alpha-D-galactoside galactohydrolase / ...Alpha-D-galactosidase A / Alpha-D-galactoside galactohydrolase / Galactosylgalactosylglucosylceramidase GLA / Melibiase


Mass: 45394.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase

-
Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 776 molecules

#5: Chemical ChemComp-VO0 / (2~{R},3~{R},4~{S},5~{R})-2-(aminomethyl)-5-(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol


Mass: 176.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 67902 / % possible obs: 98 % / Redundancy: 10.4 % / Biso Wilson estimate: 24.98 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 20.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.42 / Num. unique obs: 5624

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R47

1r47


Resolution: 2→29.49 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6542
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1862 1976 3.06 %
Rwork0.1574 62700 -
obs0.1583 64676 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.62 Å2
Refinement stepCycle: LAST / Resolution: 2→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 239 770 7270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00466673
X-RAY DIFFRACTIONf_angle_d0.80589063
X-RAY DIFFRACTIONf_chiral_restr0.0488979
X-RAY DIFFRACTIONf_plane_restr0.00571147
X-RAY DIFFRACTIONf_dihedral_angle_d14.00912440
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.33433712441 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2514740.19852571X-RAY DIFFRACTION54.17
2.05-2.110.2242960.18143152X-RAY DIFFRACTION67.08
2.11-2.170.22331350.18514104X-RAY DIFFRACTION87.31
2.17-2.240.21991500.17114685X-RAY DIFFRACTION99
2.24-2.320.18461490.17254745X-RAY DIFFRACTION99.98
2.32-2.410.18651510.15864743X-RAY DIFFRACTION100
2.41-2.520.20661480.15834732X-RAY DIFFRACTION99.94
2.52-2.660.21481530.15064791X-RAY DIFFRACTION100
2.66-2.820.18481520.15274762X-RAY DIFFRACTION99.98
2.82-3.040.16221530.14664777X-RAY DIFFRACTION99.98
3.04-3.350.18651530.15484820X-RAY DIFFRACTION100
3.35-3.830.15261520.13454831X-RAY DIFFRACTION100
3.83-4.820.14861510.13524886X-RAY DIFFRACTION100
4.82-29.490.22541590.19125101X-RAY DIFFRACTION99.96
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)
10.007105819057910.009850597813550.006852241456570.01345471455080.008998826393740.002959659814910.117775716976-0.0359313440674-0.01201977831730.0395228217393-0.06235914619860.1232703433120.0351942768417-0.00810480818723.86282825247E-50.152009774784-0.02326185343270.01429372184070.2119434395070.01389634159140.16933980930231.3699080823-29.08131334133.0187151309
20.0276521172242-0.0162034745806-0.01032153087420.006143008132860.01143397643570.01243952871150.03687108088270.20426839272-0.04250986766090.00379932362054-0.002000429036120.02617955168660.106208026315-0.1884168961610.006231089157010.186948882692-0.0611739580847-0.01703838349970.306638625331-0.02242529632860.23111883428724.0250769358-32.8562939824-13.0415156582
30.08654636503040.04435044152890.03394113134380.08706944003430.03443614080040.02754301686210.08468073178330.10316616352-3.54890910701E-50.0310637390523-0.1635915362450.1107147288790.115886680822-0.230540483227-0.02820027759420.105871682169-0.01692520440750.002573038227760.278476603687-0.03919830981520.22409307858519.1112092875-30.2848965565-3.25949319756
40.0306288392031-0.00191034106510.06956727162740.07091859935760.005666344643060.3129403312750.0357400960141-0.1618581426260.0378362625009-0.0183394221708-0.06016347251690.22512030450.0225892865465-0.467010225530.002316910547920.116623928489-0.03560022364060.03267275845260.331628244049-0.02282433836140.25870890992618.1968786813-25.52082157982.73772972103
50.0814001971958-0.02588025402890.06675935341520.0137321378657-0.01283278534050.05766051092170.0324258025308-0.1726883721280.1449910138520.103164521675-0.09156994668050.0395548027308-0.0960079822091-0.279357294334-0.05403449829540.1913543877590.004690718325230.07304714112360.288760899789-0.05381292303530.24659390644424.7972286632-16.730488928411.270908474
60.0331155251594-0.01230672135730.001178463276140.01089242789890.009922502434120.0123774940867-0.0163210130523-0.09163149054770.1508044614720.0527487909399-0.06341402655640.07956018254520.00584982515973-0.0913440692096-0.005578493253570.1574638715590.01493072818810.02736717920610.220066637748-0.01768668069150.1447749724333.5238987864-18.62685513477.71912403986
70.008067443880490.009077447802250.01309661926262.6463470244E-50.00640994015080.01447559130050.0432259678709-0.04136035260550.1234676190670.056050942353-0.06688648759620.0167767720034-0.0916932288511-0.1026888989063.50476188125E-60.1753952193930.0038077928950.02191586120220.1045890358940.0036586389820.15092348189842.9031487089-17.1357224916.10647836744
80.147790976870.0126266537044-0.02145717100820.0742188917117-0.002359422292560.09117750142270.06301328391260.0390153373143-0.0265120765280.0328714519502-0.0372508641201-0.03276255359920.06576973213960.03553680202060.005098411497110.1190589775950.00562266544917-0.004562649573990.09703223023090.01642716421280.108003034346.538846608-28.1393094680.91353830857
90.0362310580606-0.001922833166810.004738034449390.02934117439610.0318880581340.0185595494550.04288775609330.02516668651830.01155520394970.02726157981240.00871570081066-0.04484655679240.06253047959150.139135769250.02020258374990.1731086704930.0523494667987-0.028408341170.1955278066640.01455988720230.1778577938661.3027324699-26.08198405655.42121426748
100.0550467952723-0.02148736446070.03982055069590.0129194276491-0.009558053883710.03069785493680.03539912769050.0324513295195-0.08084294280910.08346715547350.0587673822809-0.08470171621670.1365127421480.1562686452310.02201424020620.1749159521210.0723051131706-0.04129931096920.1629516308760.003183766712720.14631211118662.0642437338-31.37873814075.41945139046
110.143722655353-0.054651047703-0.0004219331957490.0261523358351-0.03804884277210.166097158837-0.005822784217960.1718364225720.0370204819639-0.042607185775-0.102589235305-0.1577049224170.1098999278930.412944631072-0.07085851799580.1402809145650.0440823694560.02591054029040.3049985701040.07613551597220.21014531370170.1261843463-21.5737920666-24.6114389837
120.139161046491-0.09091435214340.1054522303760.0564755281918-0.08342110305110.215565488174-0.02434620412840.17183677107-0.0136698598449-0.0219259311051-0.18977342515-0.180821859770.000758049691380.231418283612-0.0912258873870.1065833142270.04509259590650.07136096764520.5517158049630.1692033421550.35166109712480.78046018-19.0763087532-27.235763147
130.0901436460250.00976313239875-0.005504218542820.00177590319372-0.006152429147550.106422957365-0.1172079064580.1222459170370.08288395942870.0167550961534-0.177939413858-0.21968613323-0.09657877233710.234121754754-0.1998779961840.0561186231803-0.3316009360940.01445354617020.362657823820.3461455332360.35467503414376.5122039069-6.19186021653-28.419789506
140.0924693429-0.04108696525540.009893106111520.0650437460499-0.02655805288690.122212738761-0.265825893250.1800093950870.156126624278-0.0606841257008-0.154683034431-0.186161835251-0.09792082689830.295855135173-0.4000014284310.260306207887-0.211823644930.008425702842550.207066630340.4088709805820.29628329644267.7678478259-2.13137244627-34.0664788432
150.02048374858870.00108986413525-0.001324169391740.00659144729489-0.001088352721020.000842399444015-0.1401000574720.05858788164130.171108335503-0.0636689057591-0.00195626955964-0.00888696407713-0.1009001055830.111563065781-0.03679146955340.23658069998-0.0424511824662-0.01553380234150.1999750513860.1167054236910.22948773235259.7553624405-7.1643030562-31.8631119184
160.07254739311810.105806921660.03755523178160.1657697606310.01274868560960.181386274241-0.08727347188030.08079036419670.199909635864-0.0863055425949-0.04314953646080.0161084350862-0.130467433150.0754224231207-0.09401818573250.2219637958540.05476417587720.002207676546650.1426221177560.08760395946430.16814049985550.2400462161-8.69721683356-30.5816205001
170.013541630977-0.00878199903281-0.003162776546930.004392295912650.002016769138550.0095825426027-0.00265642361857-0.02104845591350.0464989723518-0.07187979849110.00637299135102-0.039365778903-0.02862296819590.06326222781590.008050829484860.1408090240040.03412599793310.01119534982140.1340836108060.02305838882830.13699244512351.6129889042-21.6570821778-23.6795060856
180.0260591823850.00313948122933-0.007878514673580.00606407755826-0.005131134744770.008029838812710.03444270272330.0819077197069-0.0526143950046-0.0954440282977-0.0509834975544-0.07258824768970.06325686941260.124064585776-0.002439774447430.1662776958130.05537794654350.01658026498150.1573524121350.03726235725480.14944890680856.7658016873-27.0250952878-27.9697562518
190.07279541634210.04422159552790.03610710300810.0740329316531-0.0136875404250.04037530731920.0205383724290.06889437280520.0723858572133-0.122700486537-0.0199884790370.102336967332-0.0607591571114-0.176640866792-0.0359298483970.1919582564560.0562372105276-0.0185372728830.2257408609480.03712643504490.12422313014738.8047351867-18.8695228261-35.2216081586
200.01835735161840.0031908584319-0.0004900303572570.007791214933460.002987931919710.006810080242450.0462809125020.0446058903664-0.0410085631819-0.09697926485550.004251114949310.1100104682550.0339619888825-0.1564770316790.00126249790330.212920747795-0.0040998575396-0.06081101721370.2548362591480.03423233326260.16028015834335.0827748524-26.9875641161-37.3149952896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 50 )AA32 - 501 - 19
22chain 'A' and (resid 51 through 78 )AA51 - 7820 - 47
33chain 'A' and (resid 79 through 116 )AA79 - 11648 - 85
44chain 'A' and (resid 117 through 176 )AA117 - 17686 - 145
55chain 'A' and (resid 177 through 215 )AA177 - 215146 - 184
66chain 'A' and (resid 216 through 235 )AA216 - 235185 - 204
77chain 'A' and (resid 236 through 264 )AA236 - 264205 - 233
88chain 'A' and (resid 265 through 355 )AA265 - 355234 - 324
99chain 'A' and (resid 356 through 388 )AA356 - 388325 - 357
1010chain 'A' and (resid 389 through 421 )AA389 - 421358 - 390
1111chain 'B' and (resid 32 through 100 )BJ32 - 1001 - 69
1212chain 'B' and (resid 101 through 136 )BJ101 - 13670 - 105
1313chain 'B' and (resid 137 through 176 )BJ137 - 176106 - 145
1414chain 'B' and (resid 177 through 215 )BJ177 - 215146 - 184
1515chain 'B' and (resid 216 through 235 )BJ216 - 235185 - 204
1616chain 'B' and (resid 236 through 264 )BJ236 - 264205 - 233
1717chain 'B' and (resid 265 through 289 )BJ265 - 289234 - 258
1818chain 'B' and (resid 290 through 320 )BJ290 - 320259 - 289
1919chain 'B' and (resid 321 through 388 )BJ321 - 388290 - 357
2020chain 'B' and (resid 389 through 423 )BJ389 - 423358 - 392

+
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://pdbjlvh1.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