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- PDB-3pe4: Structure of human O-GlcNAc transferase and its complex with a pe... -

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Basic information

Entry
Database: PDB / ID: 3pe4
TitleStructure of human O-GlcNAc transferase and its complex with a peptide substrate
Components
  • Casein kinase II subunit alpha
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / GT-B / glycosyltransferase
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / Receptor Mediated Mitophagy / Sin3-type complex / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Maturation of hRSV A proteins / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / mitophagy / negative regulation of apoptotic signaling pathway / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of Wnt signaling pathway / histone acetyltransferase complex / negative regulation of double-strand break repair via homologous recombination / positive regulation of lipid biosynthetic process / chaperone-mediated protein folding / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell migration / response to nutrient / Signal transduction by L1 / cell projection / positive regulation of translation / mitochondrial membrane / cellular response to glucose stimulus / peptidyl-threonine phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Hsp90 protein binding / response to insulin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / PML body / Wnt signaling pathway / 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 / KEAP1-NFE2L2 pathway / double-strand break repair / rhythmic process / chromatin organization / kinase activity / positive regulation of cold-induced thermogenesis / HATs acetylate histones / positive regulation of cell growth / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / protein stabilization / negative regulation of translation / non-specific serine/threonine protein kinase / regulation of cell cycle / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / DNA damage response / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / 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 1 / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha ...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 1 / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / 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: 1.95 Å
AuthorsLazarus, M.B. / Nam, Y. / Jiang, J. / Sliz, P. / Walker, S.
CitationJournal: Nature / Year: 2011
Title: Structure of human O-GlcNAc transferase and its complex with a peptide substrate.
Authors: Lazarus, M.B. / Nam, Y. / Jiang, J. / Sliz, P. / Walker, S.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)165,8439
Polymers164,7464
Non-polymers1,0975
Water15,385854
1
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)82,9695
Polymers82,3732
Non-polymers5963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-50 kcal/mol
Surface area28710 Å2
MethodPISA
2
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)82,8734
Polymers82,3732
Non-polymers5002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-40 kcal/mol
Surface area27960 Å2
MethodPISA
3
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)165,93910
Polymers164,7464
Non-polymers1,1936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10230 Å2
ΔGint-119 kcal/mol
Surface area52720 Å2
MethodPISA
4
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)165,7478
Polymers164,7464
Non-polymers1,0004
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9990 Å2
ΔGint-95 kcal/mol
Surface area51130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.6, 136.7, 153.5
Angle α, β, γ (deg.)90.0, 102.9, 90.0
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 315:619 or resseq 621:633 or resseq...
211chain C and (resseq 336:619 or resseq 621:633 or resseq...
112chain B and (resseq 13:26 )
212chain D and (resseq 13:26 )

NCS ensembles :
ID
1
2

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Components

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


Mass: 80974.508 Da / Num. of mol.: 2 / Fragment: hOGT4.5, UNP residues 323-1041
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, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide Casein kinase II subunit alpha / CK II alpha


Mass: 1398.562 Da / Num. of mol.: 2 / Fragment: UNP residues 340-352 / Source method: obtained synthetically
Details: This is a synthetically made peptide of a sequence that occurs naturally in humans
Source: (synth.) Homo sapiens (human) / References: UniProt: P68400
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 143873 / Num. obs: 141571 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.792 Å2 / Rsym value: 0.098 / Net I/σ(I): 8.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.18 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / SU ML: 0.27 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 7099 5.02 %
Rwork0.224 --
obs0.2254 141555 98.38 %
all-143886 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.408 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2691 Å20 Å23.1097 Å2
2---1.5422 Å20 Å2
3---3.8112 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11015 0 65 854 11934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711453
X-RAY DIFFRACTIONf_angle_d1.0515573
X-RAY DIFFRACTIONf_dihedral_angle_d13.3124299
X-RAY DIFFRACTIONf_chiral_restr0.0711722
X-RAY DIFFRACTIONf_plane_restr0.0052020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5385X-RAY DIFFRACTIONPOSITIONAL
12C5385X-RAY DIFFRACTIONPOSITIONAL0.024
21B95X-RAY DIFFRACTIONPOSITIONAL
22D95X-RAY DIFFRACTIONPOSITIONAL0.017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.27792040.21863993X-RAY DIFFRACTION87
1.9722-1.99540.24562240.20594211X-RAY DIFFRACTION93
1.9954-2.01970.23212440.19344369X-RAY DIFFRACTION96
2.0197-2.04530.2592390.19174510X-RAY DIFFRACTION99
2.0453-2.07220.22822170.18894484X-RAY DIFFRACTION100
2.0722-2.10050.24852100.19874559X-RAY DIFFRACTION99
2.1005-2.13050.25182440.20214555X-RAY DIFFRACTION99
2.1305-2.16230.22372320.20044515X-RAY DIFFRACTION99
2.1623-2.19610.25382420.20094500X-RAY DIFFRACTION100
2.1961-2.23210.24592430.20834501X-RAY DIFFRACTION99
2.2321-2.27060.27542580.21224502X-RAY DIFFRACTION99
2.2706-2.31190.25492380.21354531X-RAY DIFFRACTION99
2.3119-2.35630.25042200.21544553X-RAY DIFFRACTION99
2.3563-2.40440.27962550.21784493X-RAY DIFFRACTION100
2.4044-2.45660.25042710.21054494X-RAY DIFFRACTION99
2.4566-2.51380.25022360.21324518X-RAY DIFFRACTION99
2.5138-2.57660.25162480.21824527X-RAY DIFFRACTION99
2.5766-2.64620.25012200.2154541X-RAY DIFFRACTION100
2.6462-2.7240.25812050.22114572X-RAY DIFFRACTION99
2.724-2.81190.26222190.22794551X-RAY DIFFRACTION99
2.8119-2.91230.24862430.23114503X-RAY DIFFRACTION99
2.9123-3.02880.25912590.2324543X-RAY DIFFRACTION100
3.0288-3.16650.23912360.22644509X-RAY DIFFRACTION99
3.1665-3.33330.24932480.22664524X-RAY DIFFRACTION99
3.3333-3.54180.25312480.2184540X-RAY DIFFRACTION99
3.5418-3.81470.20542540.20864514X-RAY DIFFRACTION99
3.8147-4.19770.22882280.20344534X-RAY DIFFRACTION99
4.1977-4.8030.22982450.20964480X-RAY DIFFRACTION97
4.803-6.04310.26772260.24214291X-RAY DIFFRACTION94
6.0431-29.98480.27972430.29274539X-RAY DIFFRACTION98
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)
10.5936-0.3760.60481.1915-0.31810.6495-0.2556-0.26520.0664-0.39640.13760.3005-0.1781-0.2927-0.02220.2910.0299-0.04860.39860.16650.2869-13.889436.3908-36.2853
20.24390.0847-0.58560.3048-0.1251.43060.1593-0.1505-0.1005-0.460.22250.21350.27750.1082-0.13120.3222-0.0091-0.09710.29230.08840.1766-6.39632.4652-37.3097
30.8692-0.1359-0.17210.46860.0485-0.01590.05050.22140.04480.01040.07390.0031-0.0291-0.0667-0.07940.07230.03190.02720.08070.04050.0208-5.135341.0682-14.9635
40.2272-0.03710.13560.4407-0.2790.33860.12550.09680.0608-0.0866-0.00620.02550.0417-0.0399-0.04290.1260.07090.03190.0610.03890.05-25.207944.3529-2.8034
50.1734-0.1089-0.10740.789-0.04170.34040.0770.0971-0.0097-0.2713-0.04990.06350.10110.0108-0.02340.15940.0421-0.03660.0707-0.00560.0029-25.51116.7233-2.2769
60.06260.1817-0.19940.9437-0.5150.6885-0.04530.0265-0.00980.304-0.0152-0.1264-0.1840.00780.04180.87840.2122-0.38290.39420.01220.4165-15.825429.881643.8851
70.2386-0.2708-0.21540.47340.1780.1641-0.0863-0.0932-0.11330.38020.05040.2568-0.0344-0.04810.02530.19060.03250.0590.10530.02990.0329-17.236917.944538.5677
80.98760.23920.23140.7333-0.21030.1153-0.0414-0.46830.20820.63750.18630.1320.0234-0.1135-0.06220.22960.0143-0.05630.1588-0.07550.0258-11.685422.32940.007
90.290.029-0.00620.4289-0.07320.22180.0477-0.00190.08320.0583-0.01370.0904-0.0271-0.0030.00010.06260.01970.02530.0176-0.0216-0.0153-22.610831.094622.1111
100.03610.03590.05910.06610.10610.12590.00410.0164-0.0517-0.0178-0.03650.15140.0438-0.14190.00390.1576-0.0078-0.09590.1526-0.03050.1183-41.712713.2751-4.6504
110.4602-0.11510.30880.1707-0.32110.53960.06320.04110.3422-0.1739-0.1417-0.16040.04760.0345-0.01940.13230.01960.03170.09990.0110.116-12.185429.86984.3781
120.0127-0.3199-0.19420.8256-0.11751.0839-0.0738-0.1194-0.01290.06890.026-0.12360.0490.38260.05720.10.02510.0130.15550.02330.023418.116-28.81362.7882
130.101-0.12980.15390.2418-0.05070.0502-0.2174-0.07850.1129-0.02170.1669-0.3830.20140.00320.00480.09040.1356-0.0795-0.2370.3794-0.32565.784-33.252724.4819
140.41650.079-0.08220.744-0.05220.1469-0.0131-0.01480.06750.0108-0.0364-0.2095-0.00120.04590.05280.05020.0046-0.01880.04750.03430.06345.2595-5.485424.9157
150.6611-0.4246-0.56081.15420.36980.5286-0.0902-0.00280.01710.16780.0762-0.00010.01520.0133-0.00020.40370.0713-0.26070.43930.26930.656-41.7161-18.681320.9162
160.0875-0.118-0.14990.3545-0.00040.1869-0.0024-0.0048-0.00770.25480.04150.3699-0.0564-0.0825-0.02820.08760.02510.06250.09570.0230.1416-36.2885-6.739921.6538
170.0492-0.0587-0.01080.1142-0.00890.0157-0.1217-0.0276-0.07440.067-0.02190.03170.0102-0.12680.09360.26850.03490.1080.378-0.03740.4344-33.7586-5.07633.1547
180.25030.11880.38120.7233-0.08270.77120.0093-0.0230.0365-0.01110.17470.54930.249-0.4614-0.18180.0966-0.0479-0.06860.18040.08230.2418-39.3507-12.405612.7959
190.3869-0.06960.03550.26840.0710.1557-0.015-0.02-0.0190.0767-0.03390.05860.0423-0.0166-0.0270.0887-0.01070.01910.02570.0306-0.02-16.762-18.299826.3229
200.2392-0.3810.06720.6877-0.12580.0228-0.0287-0.02990.08110.0215-0.08940.00920.0123-0.04370.06750.1080.0636-0.0540.5171-0.11020.21941.6472-7.501345.6071
210.2153-0.08090.05490.0312-0.01780.18460.08290.07870.0799-0.1797-0.109-0.06830.32530.02250.01720.15730.02430.01150.08960.02240.0209-2.9785-18.656512.4991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 315:334)
2X-RAY DIFFRACTION2(chain A and resid 335:348)
3X-RAY DIFFRACTION3(chain A and resid 349:456)
4X-RAY DIFFRACTION4(chain A and resid 457:514)
5X-RAY DIFFRACTION5(chain A and resid 515:712)
6X-RAY DIFFRACTION6(chain A and resid 713:718)
7X-RAY DIFFRACTION7(chain A and resid 719:744)
8X-RAY DIFFRACTION8(chain A and resid 745:784)
9X-RAY DIFFRACTION9(chain A and resid 785:1007)
10X-RAY DIFFRACTION10(chain A and resid 1008:1028)
11X-RAY DIFFRACTION11(chain B and resid 1:30)
12X-RAY DIFFRACTION12(chain C and resid 336:455)
13X-RAY DIFFRACTION13(chain C and resid 456:514)
14X-RAY DIFFRACTION14(chain C and resid 515:712)
15X-RAY DIFFRACTION15(chain C and resid 713:718)
16X-RAY DIFFRACTION16(chain C and resid 719:744)
17X-RAY DIFFRACTION17(chain C and resid 745:763)
18X-RAY DIFFRACTION18(chain C and resid 764:784)
19X-RAY DIFFRACTION19(chain C and resid 785:1026)
20X-RAY DIFFRACTION20(chain C and resid 1027:1126)
21X-RAY DIFFRACTION21(chain D and resid 1:30)

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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

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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

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