[English] 日本語
Yorodumi
- PDB-4gyw: Crystal structure of human O-GlcNAc Transferase in complex with U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gyw
TitleCrystal structure of human O-GlcNAc Transferase in complex with UDP and a glycopeptide
Components
  • Casein kinase II subunit alpha
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Keywordstransferase/peptide / GT-B / Glycosyltransferase / GlcNAcylation / transferase-peptide complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / regulation of glycolytic process / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / Receptor Mediated Mitophagy / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / histone acetyltransferase complex / negative regulation of double-strand break repair via homologous recombination / mitophagy / positive regulation of lipid biosynthetic process / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / : / negative regulation of cell migration / Signal transduction by L1 / cell projection / positive regulation of translation / peptidyl-threonine phosphorylation / cellular response to glucose stimulus / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Hsp90 protein binding / PML body / Regulation of necroptotic cell death / chromatin DNA binding / Wnt signaling pathway / protein processing / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / UCH proteinases / rhythmic process / KEAP1-NFE2L2 pathway / double-strand break repair / positive regulation of cold-induced thermogenesis / kinase activity / chromatin organization / HATs acetylate histones / peptidyl-serine phosphorylation / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / glutamatergic synapse / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat domain ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLazarus, M.B. / Jiang, J. / Gloster, T.M. / Zandberg, W.F. / Vocadlo, D.J. / Walker, S.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Structural snapshots of the reaction coordinate for O-GlcNAc transferase.
Authors: Lazarus, M.B. / Jiang, J. / Gloster, T.M. / Zandberg, W.F. / Whitworth, G.E. / Vocadlo, D.J. / Walker, S.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,28511
Polymers164,7464
Non-polymers1,5397
Water17,475970
1
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0955
Polymers82,3732
Non-polymers7213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area28570 Å2
MethodPISA
2
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1916
Polymers82,3732
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area29400 Å2
MethodPISA
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules

C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,18910
Polymers164,7464
Non-polymers1,4436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7660 Å2
ΔGint-38 kcal/mol
Surface area52510 Å2
MethodPISA
4
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules

A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,38112
Polymers164,7464
Non-polymers1,6358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7720 Å2
ΔGint-37 kcal/mol
Surface area54110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.000, 137.770, 153.566
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-1673-

HOH

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 6 molecules ACBD

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGT


Mass: 80974.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide Casein kinase II subunit alpha / CK II alpha


Mass: 1398.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 3 types, 975 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M Lithium Sulfate, 0.1M Bis Tris Propane pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→43.904 Å / Num. all: 206769 / Num. obs: 206769 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 %
Reflection shellResolution: 1.7→1.79 Å / % possible all: 87.1

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.904 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 10329 5 %RANDOM
Rwork0.1872 ---
all0.1881 217098 --
obs0.1881 206769 94.15 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.181 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4153 Å20 Å22.1771 Å2
2---1.9612 Å2-0 Å2
3---0.5459 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11018 0 93 970 12081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511462
X-RAY DIFFRACTIONf_angle_d0.97215576
X-RAY DIFFRACTIONf_dihedral_angle_d13.2244315
X-RAY DIFFRACTIONf_chiral_restr0.0661718
X-RAY DIFFRACTIONf_plane_restr0.0052017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.31453000.30835791X-RAY DIFFRACTION83
1.7193-1.73950.3093090.29676054X-RAY DIFFRACTION87
1.7395-1.76080.29563050.27646168X-RAY DIFFRACTION89
1.7608-1.7830.29923580.25926132X-RAY DIFFRACTION89
1.783-1.80650.30513130.23556206X-RAY DIFFRACTION89
1.8065-1.83130.23053150.2156155X-RAY DIFFRACTION89
1.8313-1.85740.25653250.23016201X-RAY DIFFRACTION89
1.8574-1.88510.23472970.2216241X-RAY DIFFRACTION90
1.8851-1.91460.26143310.19416345X-RAY DIFFRACTION91
1.9146-1.9460.21593700.18166347X-RAY DIFFRACTION92
1.946-1.97950.21833290.18036481X-RAY DIFFRACTION93
1.9795-2.01550.20023420.17126440X-RAY DIFFRACTION93
2.0155-2.05430.20043600.17496591X-RAY DIFFRACTION95
2.0543-2.09620.19173180.18176656X-RAY DIFFRACTION95
2.0962-2.14180.24083430.2146574X-RAY DIFFRACTION95
2.1418-2.19160.20753440.20096713X-RAY DIFFRACTION96
2.1916-2.24650.19933620.17926825X-RAY DIFFRACTION98
2.2465-2.30720.21173900.17946813X-RAY DIFFRACTION99
2.3072-2.37510.20233430.17796938X-RAY DIFFRACTION99
2.3751-2.45170.21653890.18976829X-RAY DIFFRACTION100
2.4517-2.53930.2083780.18696956X-RAY DIFFRACTION100
2.5393-2.6410.223640.18856940X-RAY DIFFRACTION100
2.641-2.76120.21623340.19536943X-RAY DIFFRACTION100
2.7612-2.90670.21813490.19576983X-RAY DIFFRACTION100
2.9067-3.08880.19553860.18436874X-RAY DIFFRACTION99
3.0888-3.32720.19363600.18126938X-RAY DIFFRACTION99
3.3272-3.66190.16653960.1636844X-RAY DIFFRACTION99
3.6619-4.19140.15573470.14996779X-RAY DIFFRACTION97
4.1914-5.27930.16673380.15586576X-RAY DIFFRACTION94
5.2793-43.91830.23443340.22626107X-RAY DIFFRACTION86
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)
10.0146-0.01740.01390.0219-0.0140.0120.0202-0.0216-0.0292-0.0640.05940.0954-0.0133-0.10340.02020.30320.0135-0.25690.43450.32330.3975-13.042935.5775-36.5121
20.2876-0.01410.15860.4047-0.15250.17290.03780.20180.0586-0.11790.06490.1652-0.0484-0.0046-0.03080.11830.0291-0.00670.24420.01790.1455-2.577735.8779-22.9261
30.02490.0488-0.03870.0653-0.02620.07070.09250.05850.1698-0.0015-0.01280.0005-0.0708-0.0232-0.02370.13730.05110.08070.11970.05490.1592-11.907947.7776-3.7658
40.1498-0.02070.05480.3289-0.21370.29610.0410.0770.0731-0.13870.10080.1003-0.001-0.126-0.04970.22080.0412-0.01360.19240.06740.192-28.402942.2977-6.5668
50.2411-0.01850.01340.4762-0.14010.19030.04640.09680.0141-0.2485-0.01460.07960.0653-0.03160.01030.19410.0391-0.04810.1328-0.00110.1016-25.862916.409-3.4643
60.1175-0.1693-0.05930.28750.12950.1052-0.0048-0.03230.01280.1470.00920.03650.0126-0.0081-0.00150.22410.00580.02780.1149-0.00450.1384-19.429723.385638.7429
70.3238-0.0053-0.11250.26470.03490.0622-0.0216-0.2346-0.01140.20260.05080.1460.0282-0.00350.0060.18750.0170.04960.15250.00810.1123-18.841117.759138.934
80.0022-0.00380.00030.007-0.0010.00210.015-0.13280.0520.130.0098-0.00960.1299-0.0789-0.00970.4204-0.03680.00940.4463-0.14130.1973-11.34120.977345.8929
90.26130.0212-0.09030.26450.00940.18530.0499-0.04730.09270.05430.0132-0.0189-0.05160.0077-0.00430.09770.00980.02450.0876-0.02240.1048-15.196333.056224.3721
100.05530.0248-0.0430.10020.01090.11860.0513-0.00530.04020.0267-0.02070.1466-0.0297-0.06110.02090.08970.0190.02140.1049-0.01150.1461-32.690227.91820.7683
110.058-0.03680.04010.0194-0.01870.0209-0.02740.0557-0.0151-0.08850.04040.15950.004-0.1083-0.00990.1574-0.0146-0.29050.19330.00410.2071-41.150212.7835-3.318
120.06620.00170.04190.00160.00190.02790.049-0.03840.0069-0.0035-0.0124-0.0706-0.01090.057-0.01290.1109-0.00260.00240.1615-0.01410.1818-8.356527.784711.4055
130.01340.00950.00830.0060.00540.0050.03310.03070.017-0.0277-0.011-0.01620.0011-0.0139-0.0080.18050.0370.01690.23390.0470.1378-17.450232.1735-4.1756
140.0171-0.02260.02290.0323-0.03180.0337-0.0119-0.0145-0.0110.0167-0.0123-0.0585-0.02390.16090.01760.87660.0338-0.12931.2421-0.11381.026337.6917-22.10031.0601
150.13390.091-0.04970.2665-0.06650.11430.0613-0.23920.00760.1115-0.2725-0.1867-0.14450.52380.01520.1625-0.04750.01860.37960.09320.156621.1696-25.12880.2554
160.06640.0102-0.12310.0387-0.00850.2104-0.0345-0.0036-0.0346-0.0310.0045-0.01580.13430.07160.01520.1610.05230.05660.15940.03780.10397.9658-36.38877.7101
170.2071-0.14220.13480.1249-0.03360.1453-0.1126-0.0266-0.01020.08610.0169-0.07660.12310.07520.01640.16360.0558-0.00040.14220.04060.16216.2059-32.640525.4891
180.1338-0.0285-0.05520.49320.00510.3298-0.0071-0.02990.01450.0443-0.0137-0.22480.00660.11520.04320.09710.0011-0.02610.12940.03080.18916.3444-5.180324.985
190.02010.0096-0.03010.1838-0.03930.0950.0101-0.0324-0.02510.05310.00320.06430.0351-0.0750.00080.1533-0.00980.05030.13280.00510.2322-36.2233-13.394224.5259
200.14020.1234-0.21020.3135-0.05940.4670.0215-0.00080.08330.11710.00150.1197-0.0339-0.2049-0.02640.12330.00260.03290.15950.02230.1838-36.3184-5.237722.8935
210.0499-0.09540.03730.1866-0.06810.0282-0.0550.05590.07990.00910.06040.16650.0558-0.24470.00840.1871-0.03390.01620.314-0.00510.3565-42.03-9.135719.9001
220.1685-0.0693-0.00740.26710.02740.2567-0.04220.0075-0.042-0.0086-0.00370.07010.0829-0.0431-0.04350.0939-0.0160.02240.08730.01380.1045-23.0386-21.788917.6068
230.0619-0.0007-0.02620.06660.01810.0155-0.0291-0.05310.00430.1331-0.0089-0.0102-0.02510.05160.01810.1340.00130.0140.10560.03010.0909-12.1463-18.402132.6911
240.1668-0.0432-0.01690.2910.02120.1106-0.1331-0.21360.14340.47840.07160.0165-0.0025-0.0167-0.02930.1413-0.01840.00010.0920.03770.0307-10.2985-10.987637.5303
250.0717-0.0397-0.04030.04210.0140.0694-0.0130.0522-0.0061-0.0324-0.0519-0.0180.0118-0.0470.01160.1575-0.0130.01680.16010.01760.1345-10.5786-16.64499.4018
260.0233-0.004-0.00230.0210.03240.0857-0.02360.0038-0.0105-0.0321-0.0281-0.01940.01370.01880.01060.18780.0350.02310.1970.00830.18766.0175-20.979316.5844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 314:339 )A314 - 339
2X-RAY DIFFRACTION2( CHAIN A AND RESID 340:410 )A340 - 410
3X-RAY DIFFRACTION3( CHAIN A AND RESID 411:474 )A411 - 474
4X-RAY DIFFRACTION4( CHAIN A AND RESID 475:515 )A475 - 515
5X-RAY DIFFRACTION5( CHAIN A AND RESID 516:705 )A516 - 705
6X-RAY DIFFRACTION6( CHAIN A AND RESID 706:718 )A706 - 718
7X-RAY DIFFRACTION7( CHAIN A AND RESID 719:766 )A719 - 766
8X-RAY DIFFRACTION8( CHAIN A AND RESID 767:772 )A767 - 772
9X-RAY DIFFRACTION9( CHAIN A AND RESID 773:917 )A773 - 917
10X-RAY DIFFRACTION10( CHAIN A AND RESID 918:1004 )A918 - 1004
11X-RAY DIFFRACTION11( CHAIN A AND RESID 1005:1028 )A1005 - 1028
12X-RAY DIFFRACTION12( CHAIN B AND RESID 13:20 )B13 - 20
13X-RAY DIFFRACTION13( CHAIN B AND RESID 21:26 )B21 - 26
14X-RAY DIFFRACTION14( CHAIN C AND RESID 336:348 )C336 - 348
15X-RAY DIFFRACTION15( CHAIN C AND RESID 349:408 )C349 - 408
16X-RAY DIFFRACTION16( CHAIN C AND RESID 409:460 )C409 - 460
17X-RAY DIFFRACTION17( CHAIN C AND RESID 461:515 )C461 - 515
18X-RAY DIFFRACTION18( CHAIN C AND RESID 516:705 )C516 - 705
19X-RAY DIFFRACTION19( CHAIN C AND RESID 706:721 )C706 - 721
20X-RAY DIFFRACTION20( CHAIN C AND RESID 722:763 )C722 - 763
21X-RAY DIFFRACTION21( CHAIN C AND RESID 764:772 )C764 - 772
22X-RAY DIFFRACTION22( CHAIN C AND RESID 773:913 )C773 - 913
23X-RAY DIFFRACTION23( CHAIN C AND RESID 914:958 )C914 - 958
24X-RAY DIFFRACTION24( CHAIN C AND RESID 959:1028 )C959 - 1028
25X-RAY DIFFRACTION25( CHAIN D AND RESID 13:20 )D13 - 20
26X-RAY DIFFRACTION26( CHAIN D AND RESID 21:26 )D21 - 26

+
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