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- PDB-2q3e: Structure of human UDP-glucose dehydrogenase complexed with NADH ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2q3e
TitleStructure of human UDP-glucose dehydrogenase complexed with NADH and UDP-glucose
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / UDP-GLUCOSE 6-DEHYDROGENASE / hexamer / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development / NAD binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKavanagh, K.L. / Guo, K. / Bunkoczi, G. / Savitsky, P. / Pilka, E. / Bhatia, C. / Smee, C. / Berridge, G. / von Delft, F. / Wiegelt, J. ...Kavanagh, K.L. / Guo, K. / Bunkoczi, G. / Savitsky, P. / Pilka, E. / Bhatia, C. / Smee, C. / Berridge, G. / von Delft, F. / Wiegelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and mechanism of human UDP-glucose 6-dehydrogenase.
Authors: Egger, S. / Chaikuad, A. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 31, 2011Group: Database references
Revision 1.4Oct 30, 2013Group: Non-polymer description
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.7Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
I: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
K: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)640,20748
Polymers625,00112
Non-polymers15,20636
Water49,4512745
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,10424
Polymers312,5016
Non-polymers7,60318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38500 Å2
ΔGint-313 kcal/mol
Surface area91990 Å2
MethodPISA
2
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
I: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
K: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,10424
Polymers312,5016
Non-polymers7,60318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38610 Å2
ΔGint-314 kcal/mol
Surface area91750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.990, 184.132, 170.943
Angle α, β, γ (deg.)90.00, 109.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131A
141B
151C
161D
171E
181F
191G
201H
211I
221J
231K
241L
251A
261B
271C
281D
291E
301F
311G
321H
331I
341J
351K
361L
371A
381B
391C
401D
411E
421F
431G
441H
451I
461J
471K
481L
491A
501B
511C
521D
531E
541F
551G
561H
571I
581J
591K
601L
611A
621B
631C
641D
651E
661F
671G
681H
691I
701J
711K
721L

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARGAA4 - 1155 - 116
21ILEILEARGARGBB4 - 1155 - 116
31ILEILEARGARGCC4 - 1155 - 116
41ILEILEARGARGDD4 - 1155 - 116
51ILEILEARGARGEE4 - 1155 - 116
61ILEILEARGARGFF4 - 1155 - 116
71ILEILEARGARGGG4 - 1155 - 116
81ILEILEARGARGHH4 - 1155 - 116
91ILEILEARGARGII4 - 1155 - 116
101ILEILEARGARGJJ4 - 1155 - 116
111ILEILEARGARGKK4 - 1155 - 116
121ILEILEARGARGLL4 - 1155 - 116
132ILEILEGLUGLUAA125 - 138126 - 139
142ILEILEGLUGLUBB125 - 138126 - 139
152ILEILEGLUGLUCC125 - 138126 - 139
162ILEILEGLUGLUDD125 - 138126 - 139
172ILEILEGLUGLUEE125 - 138126 - 139
182ILEILEGLUGLUFF125 - 138126 - 139
192ILEILEGLUGLUGG125 - 138126 - 139
202ILEILEGLUGLUHH125 - 138126 - 139
212ILEILEGLUGLUII125 - 138126 - 139
222ILEILEGLUGLUJJ125 - 138126 - 139
232ILEILEGLUGLUKK125 - 138126 - 139
242ILEILEGLUGLULL125 - 138126 - 139
253LEULEUTHRTHRAA157 - 211158 - 212
263LEULEUTHRTHRBB157 - 211158 - 212
273LEULEUTHRTHRCC157 - 211158 - 212
283LEULEUTHRTHRDD157 - 211158 - 212
293LEULEUTHRTHREE157 - 211158 - 212
303LEULEUTHRTHRFF157 - 211158 - 212
313LEULEUTHRTHRGG157 - 211158 - 212
323LEULEUTHRTHRHH157 - 211158 - 212
333LEULEUTHRTHRII157 - 211158 - 212
343LEULEUTHRTHRJJ157 - 211158 - 212
353LEULEUTHRTHRKK157 - 211158 - 212
363LEULEUTHRTHRLL157 - 211158 - 212
374SERSERTYRTYRAA216 - 286217 - 287
384SERSERTYRTYRBB216 - 286217 - 287
394SERSERTYRTYRCC216 - 286217 - 287
404SERSERTYRTYRDD216 - 286217 - 287
414SERSERTYRTYREE216 - 286217 - 287
424SERSERTYRTYRFF216 - 286217 - 287
434SERSERTYRTYRGG216 - 286217 - 287
444SERSERTYRTYRHH216 - 286217 - 287
454SERSERTYRTYRII216 - 286217 - 287
464SERSERTYRTYRJJ216 - 286217 - 287
474SERSERTYRTYRKK216 - 286217 - 287
484SERSERTYRTYRLL216 - 286217 - 287
495TRPTRPHISHISAA300 - 382301 - 383
505TRPTRPHISHISBB300 - 382301 - 383
515TRPTRPHISHISCC300 - 382301 - 383
525TRPTRPSERSERDD300 - 381301 - 382
535TRPTRPHISHISEE300 - 382301 - 383
545TRPTRPHISHISFF300 - 382301 - 383
555TRPTRPHISHISGG300 - 382301 - 383
565TRPTRPHISHISHH300 - 382301 - 383
575TRPTRPHISHISII300 - 382301 - 383
585TRPTRPHISHISJJ300 - 382301 - 383
595TRPTRPHISHISKK300 - 382301 - 383
605TRPTRPHISHISLL300 - 382301 - 383
616VALVALLYSLYSAA391 - 465392 - 466
626VALVALLYSLYSBB391 - 465392 - 466
636VALVALLYSLYSCC391 - 465392 - 466
646VALVALLYSLYSDD391 - 465392 - 466
656VALVALLYSLYSEE391 - 465392 - 466
666VALVALLYSLYSFF391 - 465392 - 466
676VALVALLYSLYSGG391 - 465392 - 466
686VALVALLYSLYSHH391 - 465392 - 466
696VALVALLYSLYSII391 - 465392 - 466
706VALVALLYSLYSJJ391 - 465392 - 466
716VALVALLYSLYSKK391 - 465392 - 466
726VALVALLYSLYSLL391 - 465392 - 466

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Components

#1: Protein
UDP-glucose 6-dehydrogenase / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH


Mass: 52083.418 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: pBEN1-SGC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2745 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG 3350, 8% EG, 160 mM NaBr, 80 mM BTP., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 452865 / Num. obs: 452865 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2 / Num. unique all: 65636 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o3j
Resolution: 2→49.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.545 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20521 23473 5.2 %THIN SHELLS
Rwork0.17163 ---
all0.17343 429343 --
obs0.17343 429343 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.333 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å22.37 Å2
2---1.26 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42755 0 972 2745 46472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02244763
X-RAY DIFFRACTIONr_bond_other_d0.0010.0229977
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.98760873
X-RAY DIFFRACTIONr_angle_other_deg0.9433.00172971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24455544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97624.2231930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.539157596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.94815293
X-RAY DIFFRACTIONr_chiral_restr0.0780.27054
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0249120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028796
X-RAY DIFFRACTIONr_nbd_refined0.1940.28921
X-RAY DIFFRACTIONr_nbd_other0.1850.231465
X-RAY DIFFRACTIONr_nbtor_refined0.1720.221880
X-RAY DIFFRACTIONr_nbtor_other0.0820.222357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.22676
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.647328650
X-RAY DIFFRACTIONr_mcbond_other0.57311179
X-RAY DIFFRACTIONr_mcangle_it2.275544553
X-RAY DIFFRACTIONr_scbond_it3.894818731
X-RAY DIFFRACTIONr_scangle_it5.2661116295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5174 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.190.5
2Bmedium positional0.190.5
3Cmedium positional0.210.5
4Dmedium positional0.210.5
5Emedium positional0.20.5
6Fmedium positional0.190.5
7Gmedium positional0.190.5
8Hmedium positional0.210.5
9Imedium positional0.210.5
10Jmedium positional0.190.5
11Kmedium positional0.210.5
12Lmedium positional0.190.5
1Amedium thermal0.722
2Bmedium thermal0.672
3Cmedium thermal0.732
4Dmedium thermal0.652
5Emedium thermal0.732
6Fmedium thermal0.652
7Gmedium thermal0.672
8Hmedium thermal0.622
9Imedium thermal0.672
10Jmedium thermal0.622
11Kmedium thermal0.662
12Lmedium thermal0.592
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.238 33139 -
Rfree-0 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6443-0.1295-0.22390.57340.21330.39550.0160.03090.0456-0.08080.0102-0.07290.00920.0412-0.0263-0.08920.0199-0.0166-0.1234-0.0142-0.1219-23.668-10.138-71.916
21.3692-0.1122-0.23590.4130.01760.3819-0.0056-0.28440.11090.0480.0178-0.15610.01150.1634-0.0122-0.12080.0095-0.04680.0577-0.0404-0.0544-10.17-3.336-36.627
30.49940.0953-0.22580.7784-0.27310.32950.00320.03740.089-0.04520.01910.0671-0.0425-0.0594-0.0223-0.06170.002-0.0342-0.10620.0137-0.1033-59.23727.447-61.321
40.545-0.1442-0.23220.94850.08080.47770.0101-0.18760.19950.13490.0534-0.0784-0.07880.0446-0.0635-0.03070.0081-0.0103-0.0052-0.1031-0.078-51.10327.421-23.673
50.8428-0.104-0.2440.540.09730.3423-0.06210.0419-0.177-0.0368-0.01860.14970.0941-0.09950.0807-0.1075-0.0258-0.052-0.0558-0.0132-0.0513-71.491-23.654-54.175
60.68750.0641-0.13460.727-0.27270.6653-0.0161-0.1662-0.11410.0987-0.05830.02880.13830.00320.0744-0.02540.00450.0035-0.00170.0704-0.1181-55.087-24.88-19.113
70.7591-0.2374-0.31550.73950.29580.44140.0490.04610.0574-0.1224-0.0136-0.1152-0.02930.0338-0.0354-0.0690.0111-0.0082-0.108-0.0262-0.08225.966-7.7678.375
81.3797-0.1576-0.32790.62020.09280.46950.0061-0.41770.06770.06970.0417-0.23280.01880.2691-0.0479-0.0984-0.0084-0.05570.1752-0.04590.006619.478-1.77243.788
90.45050.1249-0.21330.8876-0.29620.35280.02260.06130.1184-0.0595-0.00020.072-0.0435-0.0685-0.0223-0.02830.0021-0.0269-0.09630.0104-0.0788-29.49129.70619.916
100.7298-0.0006-0.30650.93510.04330.58610.0739-0.21260.20140.1496-0.0023-0.0188-0.11910.103-0.07160.0074-0.04560.0111-0.0186-0.1017-0.089-21.22728.91257.594
110.9315-0.0323-0.21720.60320.05330.3859-0.07890.104-0.1977-0.0041-0.01890.13470.1259-0.14010.0977-0.0869-0.0444-0.0365-0.0358-0.0628-0.0126-41.954-21.4425.608
120.70840.1098-0.24740.698-0.20790.7029-0.0537-0.1997-0.22150.133-0.08140.03420.1850.07840.13510.03080.01770.0236-0.00520.0955-0.0347-25.676-23.54260.621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4662 - 467
2X-RAY DIFFRACTION2BB1 - 4662 - 467
3X-RAY DIFFRACTION3CC1 - 4662 - 467
4X-RAY DIFFRACTION4DD2 - 4663 - 467
5X-RAY DIFFRACTION5EE2 - 4663 - 467
6X-RAY DIFFRACTION6FF1 - 4662 - 467
7X-RAY DIFFRACTION7GG1 - 4662 - 467
8X-RAY DIFFRACTION8HH2 - 4663 - 467
9X-RAY DIFFRACTION9II1 - 4662 - 467
10X-RAY DIFFRACTION10JJ1 - 4662 - 467
11X-RAY DIFFRACTION11KK1 - 4662 - 467
12X-RAY DIFFRACTION12LL1 - 4662 - 467

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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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