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- PDB-8v06: Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA f... -

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Basic information

Entry
Database: PDB / ID: 8v06
TitleCrystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days
Components(5'-3' exonuclease ...) x 2
KeywordsHYDROLASE / PLD3 / phospholipase / phosphohistidine / nuclease
Function / homology
Function and homology information


spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response ...spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane
Similarity search - Function
PLD-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
PHOSPHATE ION / 5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142945 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG070775 United States
CitationJournal: Structure / Year: 2024
Title: Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4.
Authors: Yuan, M. / Peng, L. / Huang, D. / Gavin, A. / Luan, F. / Tran, J. / Feng, Z. / Zhu, X. / Matteson, J. / Wilson, I.A. / Nemazee, D.
History
DepositionNov 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-3' exonuclease PLD3
B: 5'-3' exonuclease PLD3
C: 5'-3' exonuclease PLD3
D: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,69314
Polymers207,5834
Non-polymers4,11110
Water3,369187
1
A: 5'-3' exonuclease PLD3
B: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9268
Polymers103,7912
Non-polymers2,1356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint16 kcal/mol
Surface area32270 Å2
MethodPISA
2
C: 5'-3' exonuclease PLD3
D: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7676
Polymers103,7912
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint13 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.155, 54.191, 202.774
Angle α, β, γ (deg.)96.61, 89.16, 90.10
Int Tables number1
Space group name H-MP1

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Components

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5'-3' exonuclease ... , 2 types, 4 molecules ACBD

#1: Protein 5'-3' exonuclease PLD3


Mass: 51935.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405
#2: Protein 5'-3' exonuclease PLD3


Mass: 51856.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405

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Sugars , 4 types, 8 molecules

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


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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 189 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.5 mM magnesium chloride, 0.1 M citric acid, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.73→60 Å / Num. obs: 57208 / % possible obs: 95.5 % / Redundancy: 3 % / CC1/2: 0.967 / CC star: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.08 / Rrim(I) all: 0.146 / Χ2: 1.749 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.75-2.81.90.42422150.5920.8620.340.5460.84475.9
2.8-2.852.10.37326130.6570.8910.280.4690.91384.1
2.85-2.92.40.35225960.7110.9120.2520.4350.88588.9
2.9-2.962.60.33327810.7240.9170.2330.4090.93692.1
2.96-3.032.90.27929180.830.9520.190.3391.00195.6
3.03-3.130.26228040.8380.9550.1720.3151.04996.9
3.1-3.173.10.23429970.8840.9690.1530.2811.11497.4
3.17-3.2630.21928710.8820.9680.1490.2661.17998.4
3.26-3.363.10.18529880.9090.9760.1250.2251.32397.6
3.36-3.463.20.16429280.9340.9830.1080.1971.45498.6
3.46-3.593.10.14329610.9440.9850.0970.1731.71498.1
3.59-3.733.40.1328960.9630.990.0820.1541.78398.7
3.73-3.93.50.1230500.970.9920.0750.1421.84898.6
3.9-4.113.40.10528800.9750.9940.0670.1252.12998.4
4.11-4.363.30.09529260.9780.9940.0610.1132.26598.5
4.36-4.73.10.08629530.9780.9950.0580.1052.52198.3
4.7-5.173.10.0829420.9790.9950.0550.0982.58498.1
5.17-5.923.20.08729940.9830.9960.0580.1052.3598.7
5.92-7.463.40.08329390.9860.9960.0520.0992.23798.6
7.46-603.30.05629560.9940.9980.0370.0682.69398.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→49.92 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 2641 4.62 %
Rwork0.2552 --
obs0.2572 57195 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12941 0 269 187 13397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313504
X-RAY DIFFRACTIONf_angle_d0.63918425
X-RAY DIFFRACTIONf_dihedral_angle_d6.4911946
X-RAY DIFFRACTIONf_chiral_restr0.0442102
X-RAY DIFFRACTIONf_plane_restr0.0052349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.780.4098740.32391420X-RAY DIFFRACTION48
2.78-2.830.35581440.3062608X-RAY DIFFRACTION82
2.83-2.890.40881130.30272682X-RAY DIFFRACTION89
2.89-2.950.3061300.28612868X-RAY DIFFRACTION92
2.95-3.020.34741190.27922948X-RAY DIFFRACTION96
3.02-3.10.30861090.27252923X-RAY DIFFRACTION97
3.1-3.180.34951380.28343110X-RAY DIFFRACTION98
3.18-3.270.31821120.28142942X-RAY DIFFRACTION98
3.27-3.380.32221450.27373047X-RAY DIFFRACTION98
3.38-3.50.29771750.25712936X-RAY DIFFRACTION99
3.5-3.640.2921560.24413060X-RAY DIFFRACTION98
3.64-3.80.28531470.24942976X-RAY DIFFRACTION98
3.8-4.010.28882000.23242946X-RAY DIFFRACTION99
4.01-4.260.32271210.2313054X-RAY DIFFRACTION98
4.26-4.580.23561610.22642996X-RAY DIFFRACTION98
4.58-5.050.24881480.21053011X-RAY DIFFRACTION98
5.05-5.770.2531360.2453007X-RAY DIFFRACTION99
5.77-7.270.29991450.26933014X-RAY DIFFRACTION99
7.27-49.920.29151680.27373006X-RAY DIFFRACTION98
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)
10.04340.1093-0.05370.2645-0.12830.0981-0.13-0.0080.02080.09980.03990.10940.0517-0.0002-0.25090.41730.032-0.0066-0.11160.06530.18229.079931.0024-50.7224
20.1387-0.2195-0.0960.3641-0.00931.5154-0.01370.01120.10650.14060.0618-0.1726-0.1370.03760.64740.2476-0.0393-0.17040.05690.03520.251324.468434.9366-52.7059
30.0061-0.0582-0.00060.22580.03820.0425-0.0825-0.0645-0.12910.0753-0.1158-0.09330.23110.1132-0.26650.26130.02730.0532-0.06920.15450.179216.583921.5469-60.6448
40.1721-0.24260.05950.40120.06290.36490.03060.05370.1033-0.11840.0282-0.0795-0.02820.0220.7480.2171-0.0370.0585-0.02780.08930.05456.305925.8409-77.4836
50.32090.00050.07640.1891-0.10530.3085-0.0296-0.03170.03080.0764-0.0458-0.0234-0.0781-0.0184-0.10520.1379-0.07590.0172-0.05780.03670.1950.260631.5564-74.2615
60.4762-0.07170.00960.36880.31630.2763-0.03930.09620.0864-0.12760.0350.0194-0.0513-0.0427-0.06220.0605-0.03560.07970.10720.08780.0175-5.432330.4812-67.2552
70.7965-0.0991-0.05220.2433-0.02590.1557-0.0277-0.1019-0.15980.0669-0.1038-0.03370.10680.0325-0.1945-0.17750.0412-0.05130.2111-0.00890.09393.717215.4559-120.7204
81.5524-0.96590.04582.2029-1.13733.05170.0918-0.1081-0.33560.3388-0.2017-0.06860.0929-0.09180.03290.1699-0.0427-0.00790.0666-0.00820.16094.043823.4936-99.6719
90.58390.05130.09430.2289-0.00160.207-0.07220.1587-0.05260.04720.00150.05480.047-0.0244-0.1586-0.0846-0.006-0.02110.069-0.01490.18-1.679729.6323-102.8341
101.01650.13310.23270.34160.05610.2357-0.0362-0.23480.14350.05180.01220.004-0.0074-0.05040.1033-0.0265-0.052-0.10280.20040.04650.0755-0.625535.2313-109.8754
111.66281.2326-0.5571.91480.34121.49920.2423-0.11750.3090.1541-0.24840.0377-0.05260.0022-0.03430.29220.1162-0.03950.566-0.19180.3416-5.109217.634-151.3288
121.15570.1975-0.53120.76580.23411.3966-0.1533-0.05580.1784-0.2227-0.04770.1888-0.05330.0960.10480.24930.0715-0.07850.3654-0.21390.40475.28722.2652-160.9061
132.0630.2502-0.92630.6298-1.07044.9380.07760.01610.311-0.0339-0.27050.25440.0981-0.2847-0.08550.255-0.06150.1020.4413-0.2810.48811.002812.2635-177.9945
144.30090.2182-1.18981.37410.45012.58180.5741-0.367-0.1104-0.476-0.38530.1023-0.47660.1017-0.2210.40480.0852-0.01360.4078-0.1320.3915-2.85772.6383-181.0271
151.7257-1.2715-0.7692.98160.68552.56480.14410.1249-0.0118-0.27490.09530.05060.0017-0.0932-0.22530.33250.0969-0.07730.561-0.06660.1896-6.955910.4551-166.9034
162.96631.78190.94343.19861.24662.92640.1064-0.011-0.38490.1862-0.0487-0.15570.37390.1272-0.05920.29640.06090.0470.174-0.07630.0847-3.67680.3499-167.8485
170.5517-0.1883-0.06010.06360.0340.5474-0.11460.06-0.0368-0.39940.1779-0.1885-0.15460.0040.03360.74130.05230.01810.2935-0.16420.40155.67124.7812-227.0184
181.47930.6156-0.57981.4163-0.6881.27760.0502-0.21390.0707-0.1214-0.4341-0.0221-0.19020.04060.20770.59910.0497-0.03740.3098-0.10810.385314.598712.6003-218.2386
192.51251.95390.34521.63960.94515.0066-0.11350.309-0.342-0.231-0.02130.28950.51050.68250.09830.56150.00510.0160.422-0.23830.41053.334610.2145-200.1681
201.4065-0.294-0.35942.2708-0.61711.2168-0.1879-0.0983-0.1102-0.0030.0512-0.05690.1055-0.12160.10350.4240.0252-0.06060.3899-0.1480.2683-3.76356.6769-205.5605
214.7274-1.60983.52282.7808-0.62183.77320.21530.0277-0.53210.7542-0.36260.73160.8507-0.14640.26131.0552-0.1772-0.13560.4653-0.14980.5289-10.364-7.6861-205.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 341 )
5X-RAY DIFFRACTION5chain 'A' and (resid 342 through 440 )
6X-RAY DIFFRACTION6chain 'A' and (resid 441 through 488 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 304 )
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 341 )
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 440 )
10X-RAY DIFFRACTION10chain 'B' and (resid 441 through 488 )
11X-RAY DIFFRACTION11chain 'C' and (resid 73 through 180 )
12X-RAY DIFFRACTION12chain 'C' and (resid 181 through 304 )
13X-RAY DIFFRACTION13chain 'C' and (resid 305 through 341 )
14X-RAY DIFFRACTION14chain 'C' and (resid 342 through 396 )
15X-RAY DIFFRACTION15chain 'C' and (resid 397 through 440 )
16X-RAY DIFFRACTION16chain 'C' and (resid 441 through 488 )
17X-RAY DIFFRACTION17chain 'D' and (resid 73 through 157 )
18X-RAY DIFFRACTION18chain 'D' and (resid 158 through 304 )
19X-RAY DIFFRACTION19chain 'D' and (resid 305 through 341 )
20X-RAY DIFFRACTION20chain 'D' and (resid 342 through 467 )
21X-RAY DIFFRACTION21chain 'D' and (resid 468 through 488 )

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Yorodumi

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  • 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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