[English] 日本語
Yorodumi
- PDB-5hgv: Structure of an O-GlcNAc transferase point mutant, D554N in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hgv
TitleStructure of an O-GlcNAc transferase point mutant, D554N in complex with peptide
Components
  • TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE/PEPTIDE / Point mutant / Glycosyltransferase / OGT / 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 / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / Receptor Mediated Mitophagy / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Synthesis of PC / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Sin3-type complex / positive regulation of stem cell population maintenance / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / hemopoiesis / negative regulation of apoptotic signaling pathway / histone acetyltransferase complex / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / positive regulation of lipid biosynthetic process / mitophagy / : / response to nutrient / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of cell migration / positive regulation of translation / Signal transduction by L1 / cell projection / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / chromatin DNA binding / Regulation of necroptotic cell death / circadian regulation of gene expression / response to insulin / PML body / mitochondrial membrane / Regulation of PTEN stability and activity / protein processing / Wnt signaling pathway / KEAP1-NFE2L2 pathway / UCH proteinases / positive regulation of protein catabolic process / rhythmic process / kinase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / HATs acetylate histones / positive regulation of cold-induced thermogenesis / chromatin organization / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / 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 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / 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: 2.05 Å
AuthorsJanetzko, J. / Lazarus, M.B. / Walker, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094263 United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: How the glycosyltransferase OGT catalyzes amide bond cleavage.
Authors: Janetzko, J. / Trauger, S.A. / Lazarus, M.B. / Walker, S.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,68611
Polymers164,1484
Non-polymers1,5397
Water13,908772
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8916
Polymers82,0742
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-46 kcal/mol
Surface area28780 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7955
Polymers82,0742
Non-polymers7213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-34 kcal/mol
Surface area27970 Å2
MethodPISA
3
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules

A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,78312
Polymers164,1484
Non-polymers1,6358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11420 Å2
ΔGint-110 kcal/mol
Surface area52730 Å2
MethodPISA
4
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules

C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,59010
Polymers164,1484
Non-polymers1,4436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10980 Å2
ΔGint-82 kcal/mol
Surface area51240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.350, 137.190, 153.070
Angle α, β, γ (deg.)90.000, 103.050, 90.000
Int Tables number5
Space group name H-MI121

-
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: 80675.219 Da / Num. of mol.: 2 / Mutation: D554N
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 TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET


Mass: 1398.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68400*PLUS
#5: 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: 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, 777 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.: 772 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M Lithium Sulfate, 0.1 M Bis Tris Propane pH 7.0
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.09999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09999 Å / Relative weight: 1
ReflectionResolution: 2.05→40.93 Å / Num. obs: 117637 / % possible obs: 95.2 % / Redundancy: 2.7 % / CC1/2: 0.976 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.066 / Net I/σ(I): 5.9 / Num. measured all: 313938 / Scaling rejects: 140
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.092.30.3241.91233452710.5210.24386.3
11.23-40.933.20.07810.824937810.9890.04997.9

-
Processing

Software
NameVersionClassification
SCALA0.5.12data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
CBASSdata collection
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 2.05→40.925 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 5893 5.02 %
Rwork0.2172 111524 -
obs0.2182 117417 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.28 Å2 / Biso mean: 32.3017 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 2.05→40.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11018 0 93 772 11883
Biso mean--21.8 33.6 -
Num. residues----1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411462
X-RAY DIFFRACTIONf_angle_d0.66115576
X-RAY DIFFRACTIONf_chiral_restr0.0451718
X-RAY DIFFRACTIONf_plane_restr0.0052017
X-RAY DIFFRACTIONf_dihedral_angle_d11.8566983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07330.28611610.25493366352787
2.0733-2.09770.26691520.24173348350085
2.0977-2.12330.26061810.23093362354386
2.1233-2.15020.26751790.23013380355988
2.1502-2.17840.25041780.22583478365689
2.1784-2.20830.27441880.23183412360088
2.2083-2.23980.24281790.23543464364389
2.2398-2.27330.26292120.23263494370690
2.2733-2.30880.28141910.23723565375691
2.3088-2.34660.22511750.23113626380193
2.3466-2.38710.29611990.23563662386194
2.3871-2.43050.25352010.23733714391595
2.4305-2.47720.28172280.24423730395896
2.4772-2.52780.2521880.24333786397497
2.5278-2.58270.25392170.24183794401198
2.5827-2.64280.30571850.23693851403698
2.6428-2.70890.30871720.24943887405999
2.7089-2.78210.26731950.247138984093100
2.7821-2.8640.27031970.237539294126100
2.864-2.95640.23532160.22763890410699
2.9564-3.0620.23852150.22383836405199
3.062-3.18460.25841970.226339224119100
3.1846-3.32940.24382120.21413851406398
3.3294-3.50490.21072200.20263841406199
3.5049-3.72430.20292220.19183856407899
3.7243-4.01170.1881940.18133924411899
4.0117-4.41490.19932100.17473877408798
4.4149-5.05280.20591820.18443913409599
5.0528-6.36210.22082270.21893902412999
6.3621-40.93320.23342200.23423966418699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1007-0.94582.21044.19570.3192.6633-0.1882-0.39120.1665-0.89460.30041.020.0233-1.0527-0.15860.70150.0508-0.3380.70960.17630.6763-12.791835.6321-36.4893
21.34020.22650.61963.66150.10613.10570.02370.23670.0218-0.33090.06170.3921-0.0709-0.1291-0.09260.19030.0493-0.01090.36070.01120.2289-2.510135.9428-22.8402
33.69581.0313-3.75360.6758-0.57024.60230.13450.14570.2391-0.0159-0.01320.0482-0.2389-0.0749-0.1230.24920.05210.06240.18980.04550.2355-11.797547.8391-3.7452
44.84340.38211.17775.41040.54582.01330.09170.46220.2914-0.69040.08330.3435-0.2377-0.04-0.1660.33070.0885-0.02370.28030.04890.2689-28.135942.2839-6.7159
51.0547-0.22180.042.0648-0.23671.51820.08650.27520.022-0.567-0.06660.26510.1562-0.0985-0.01610.33530.0557-0.05510.2257-0.02150.1979-25.611916.4683-3.6429
67.0996-0.5336-0.70992.7426-1.6054.8387-0.2001-1.24510.51451.1157-0.4210.6303-0.3998-0.23550.56170.5780.05290.1050.4384-0.00890.2892-19.441923.379938.5965
70.10710.0961-0.06020.9875-0.82660.6931-0.199-0.4772-0.23551.00360.2280.73830.0688-0.28640.01180.48320.04590.16630.35940.0320.3062-18.802317.742938.7543
81.47670.57461.19790.37540.29241.1617-0.2797-0.47230.50360.33750.3771-0.4345-0.56130.20190.01281.0436-0.21560.01510.9304-0.39310.4491-11.34920.964645.7467
91.2508-0.6245-0.01612.2853-0.54671.03050.0457-0.15040.19240.24450.0095-0.0951-0.14140.0336-0.04170.169-0.00210.04980.1567-0.04340.1603-15.115733.038224.2474
100.1261-0.1120.15681.07250.69881.2910.0352-0.02070.04440.1393-0.03580.42030.0173-0.16260.02450.16950.0270.0750.1938-0.02150.2818-32.543827.865820.5533
112.4663-1.41081.60870.8821-0.53962.9672-0.26920.2143-0.1298-0.22620.08631.05790.1345-0.72450.01760.4288-0.0164-0.23820.4147-0.02860.5526-40.917312.887-3.5477
123.429-0.15791.96742.8229-0.9493.25280.3574-0.0565-0.2264-0.1375-0.163-0.480.34050.5879-0.17930.15730.06230.02360.2658-0.01720.1745-8.275827.888911.3
132.82160.50942.88595.3048-1.08153.45080.12010.99860.8955-0.7475-0.1086-0.9073-0.48930.82770.04830.35930.10420.09080.39490.08420.3627-17.06632.2079-4.3305
143.88141.74920.20152.1709-0.81751.2973-0.5076-0.07580.38190.51620.1982-1.1317-0.45080.30210.29580.52180.0088-0.3721.0345-0.18351.131837.6796-22.1541.2321
154.3192-0.1363-1.29794.819-0.87762.63080.0179-0.19060.03930.3283-0.2872-0.5941-0.17811.00440.31770.2992-0.0391-0.00250.54670.08930.250421.045-25.07060.4206
162.02340.7428-2.10330.842-0.13136.2899-0.1159-0.0282-0.1078-0.02420.0234-0.00740.25330.16590.09650.28490.06310.04780.19230.01040.19717.9193-36.37097.7204
172.88930.28021.62352.49660.92262.4834-0.1075-0.0838-0.18520.30920.027-0.38130.22980.20930.06290.27430.06310.03320.22610.07950.23216.1247-32.562825.4142
181.4648-0.05320.00372.0554-0.17121.0030.0067-0.08970.10210.1157-0.0525-0.5469-0.01750.24620.04610.1736-0.0036-0.01860.19210.03590.28936.3142-5.199924.8557
196.1216-0.4710.79924.3485-1.37958.11840.1647-0.7069-0.50140.1938-0.25981.31710.7368-1.00170.09690.3534-0.00860.17030.35230.00370.5549-36.2253-13.307824.2784
202.5702-1.2092-0.77673.38640.82411.19730.0227-0.33530.12740.81630.03610.6343-0.1143-0.4185-0.07360.31580.01680.1130.31580.02460.3641-36.2657-5.149622.5898
217.50851.66144.01412.3312-0.25969.3509-0.46670.7355-0.6906-0.41570.55531.17721.0433-1.0995-0.07860.5149-0.15150.06220.5855-0.07330.7456-41.9957-9.006819.5694
221.0581-0.75660.03422.7922-0.57481.2954-0.00460.0474-0.149-0.10280.01260.37660.1956-0.1828-0.02440.1645-0.03970.03630.1529-0.00680.1716-22.996-21.714117.4134
231.3679-0.59930.32291.9683-0.28380.75640.0546-0.1647-0.01160.3272-0.06220.06990.01490.05920.01520.2731-0.01810.04040.19850.03290.1615-12.1786-18.272932.5197
241.69910.5799-0.09831.7089-0.08740.54760.0118-0.3470.20120.534-0.0693-0.00530.08130.0534-0.02020.32570.00070.03020.20640.02040.116-10.3319-10.893537.3668
255.039-2.10813.75993.3124-0.8513.82160.25820.44620.3483-0.5885-0.16270.1256-0.0755-0.1034-0.130.2507-0.01110.03850.2640.04230.1334-10.5224-16.67889.3169
265.095-5.17971.55386.92120.08173.43950.02160.6113-0.581-1.1766-0.1335-0.58010.7260.91780.06950.38490.02060.13050.3359-0.00840.35.9507-21.02216.3292
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