[English] 日本語
Yorodumi
- PDB-5iud: Human DNA polymerase alpha in binary complex with a DNA:DNA templ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iud
TitleHuman DNA polymerase alpha in binary complex with a DNA:DNA template-primer
Components
  • DNA polymerase alpha catalytic subunit
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsTransferase/DNA / DNA polymerase binary complex / Transferase-DNA complex
Function / homology
Function and homology information


DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / regulation of type I interferon production / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation ...DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / regulation of type I interferon production / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / nuclear matrix / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / nuclear envelope / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / chromatin binding / chromatin / nucleolus / protein kinase binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B ...DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsColoma, J. / Aggarwal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA 138546 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32 CA 78207-14 United States
CitationJournal: Sci Rep / Year: 2016
Title: Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer.
Authors: Coloma, J. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase alpha catalytic subunit
B: DNA template
C: DNA primer
D: DNA polymerase alpha catalytic subunit
E: DNA template
F: DNA primer
G: DNA polymerase alpha catalytic subunit
H: DNA template
I: DNA primer
J: DNA polymerase alpha catalytic subunit
K: DNA template
L: DNA primer


Theoretical massNumber of molelcules
Total (without water)456,05712
Polymers456,05712
Non-polymers00
Water1,802100
1
A: DNA polymerase alpha catalytic subunit
B: DNA template
C: DNA primer


Theoretical massNumber of molelcules
Total (without water)114,0143
Polymers114,0143
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA polymerase alpha catalytic subunit
E: DNA template
F: DNA primer


Theoretical massNumber of molelcules
Total (without water)114,0143
Polymers114,0143
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA polymerase alpha catalytic subunit
H: DNA template
I: DNA primer


Theoretical massNumber of molelcules
Total (without water)114,0143
Polymers114,0143
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: DNA polymerase alpha catalytic subunit
K: DNA template
L: DNA primer


Theoretical massNumber of molelcules
Total (without water)114,0143
Polymers114,0143
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.040, 132.030, 163.139
Angle α, β, γ (deg.)90.000, 109.130, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DNA polymerase alpha catalytic subunit / DNA polymerase alpha catalytic subunit p180


Mass: 105124.438 Da / Num. of mol.: 4 / Fragment: UNP Residues 338-1255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLA1, POLA / Production host: Escherichia coli (E. coli) / References: UniProt: P09884, DNA-directed DNA polymerase
#2: DNA chain
DNA template


Mass: 5067.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA primer / Primer (molecular biology)


Mass: 3822.500 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% polyethylene glycol 4000, 0.2M sodium citrate, 10% isopropanol, 0.1M sodium citrate buffer (pH = 5.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→86.22 Å / Num. obs: 82602 / % possible obs: 99.6 % / Redundancy: 3 % / Biso Wilson estimate: 92.8 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.056 / Rrim(I) all: 0.1 / Net I/σ(I): 7.8 / Num. measured all: 248849 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.8 % / Rejects: 0

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.370.7611302846680.5480.5350.9351.599.4
16.83-86.220.06318706680.9270.0450.07720.798.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.2.1data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→64.736 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 4118 5 %
Rwork0.1832 78196 -
obs0.1854 82314 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 283.78 Å2 / Biso mean: 108.8025 Å2 / Biso min: 32.59 Å2
Refinement stepCycle: final / Resolution: 3.3→64.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25907 2200 0 100 28207
Biso mean---73.87 -
Num. residues----3562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228931
X-RAY DIFFRACTIONf_angle_d0.4839902
X-RAY DIFFRACTIONf_chiral_restr0.0394653
X-RAY DIFFRACTIONf_plane_restr0.0034764
X-RAY DIFFRACTIONf_dihedral_angle_d10.97516912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.33880.32131480.26292683283199
3.3388-3.37950.34871640.24782645280999
3.3795-3.42230.29921390.25032652279199
3.4223-3.46740.31381480.234326612809100
3.4674-3.51480.28421510.229126942845100
3.5148-3.56510.27261250.21922715284099
3.5651-3.61830.25161370.215326792816100
3.6183-3.67480.27371430.22562684282799
3.6748-3.7350.34911290.22292690281999
3.735-3.79940.26391350.21382649278499
3.7994-3.86850.28451250.20392695282099
3.8685-3.94290.25961460.19492642278899
3.9429-4.02340.23921270.18972721284899
4.0234-4.11090.24541290.180127172846100
4.1109-4.20650.24631370.17792670280799
4.2065-4.31160.22731540.17162672282699
4.3116-4.42820.21121530.168227012854100
4.4282-4.55850.22041620.163226972859100
4.5585-4.70560.19551180.149127052823100
4.7056-4.87370.19841430.141727352878100
4.8737-5.06870.20441550.154326612816100
5.0687-5.29930.21141370.16452703284099
5.2993-5.57860.23051430.179926902833100
5.5786-5.92790.21691380.186227272865100
5.9279-6.38520.27561360.20227262862100
6.3852-7.02710.27391560.194927282884100
7.0271-8.04230.19371350.166627512886100
8.0423-10.12620.16581590.151227302889100
10.1262-64.74860.17531460.18282773291999
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)
13.6431-0.3944-0.79641.83190.51412.9889-0.04170.9172-0.4959-0.390.00770.18760.8412-0.2530.11470.734-0.0765-0.13040.6031-0.11080.5751-11.215217.3136136.306
25.48461.706-1.10944.8285-1.17357.83840.3063-0.85-0.14610.6698-0.26780.49771.0427-0.6354-0.04930.7245-0.12050.01050.6147-0.07830.5195-22.762523.4914166.3595
35.6370.2314-1.84613.3314-0.3227.2065-0.0053-1.1784-0.12910.8024-0.0726-0.10970.6661-0.1280.18130.66510.018-0.10250.62470.02720.4769-8.078529.6937166.846
47.85211.57522.9892.4737-0.06314.83160.1072-0.51950.58480.1652-0.5128-0.25140.0387-0.24220.42040.5540.16680.07860.3647-0.11750.471517.058928.7523150.3731
58.57523.79011.7973.8851-1.83483.4859-0.31651.82420.7425-0.6658-0.0485-0.5532-0.06820.86360.41710.66930.1676-0.0410.82860.0950.608918.278729.2253137.5841
64.8731-0.5780.19151.4085-0.72722.0191-0.1071-0.16930.96350.1853-0.0834-0.2642-0.28360.03220.20750.6160.0281-0.06530.3822-0.0060.742918.536638.5403151.5618
75.19962.9797-1.23915.7276-0.3943.42770.0866-1.31820.08770.99830.03060.1845-0.306-0.1521-0.08180.79240.3336-0.10571.14110.01260.684113.376928.1359181.0206
84.64655.72164.28746.94855.28884.08740.0355-1.25361.36140.9253-0.36571.03550.6722-1.59420.37210.80280.1086-0.01020.95250.11730.83712.625720.8553156.1153
94.0515-4.90312.57839.7336-4.46454.3583-0.16740.7891-0.47961.29060.1580.51-0.3351-0.1575-0.00190.72120.0991-0.07691.21450.16740.849624.258911.1422174.3807
103.7142-2.70683.91979.5459-6.195.61930.80522.13060.00571.11940.74570.7907-1.54171.4462-1.47041.13060.20620.00361.43620.1550.681131.90567.7322177.4067
111.2267-2.70023.28179.9116-6.69219.00670.26150.2226-0.7013-1.571-0.62640.69530.08940.02240.40360.70610.305-0.10981.11550.06521.013516.989220.081167.1295
122.55660.40450.42251.71530.55342.9503-0.11780.8856-0.031-0.647-0.0660.5893-0.2693-0.47020.06730.5595-0.0027-0.20580.8199-0.07830.7243-30.31959.6773125.4347
133.17312.15870.78444.52490.34332.37080.1124-0.33350.34480.1144-0.19870.4125-0.3051-0.1960.05560.33450.0166-0.01130.5099-0.10760.6121-18.98171.7448152.1209
141.5844-0.5798-0.66661.38870.53791.3979-0.1111-0.20090.03450.2110.08190.4339-0.1734-0.23070.03840.60830.0683-0.0590.9406-0.10251.5034-51.566364.7322157.3854
156.1665-5.6339-6.00035.19255.51045.8460.7572-0.01981.33-0.16460.6279-0.4302-1.10830.3646-1.30890.93270.10150.00641.109-0.3211.7168-54.595273.9048151.9353
165.71532.1508-1.3864.42132.50362.88760.67190.6662-3.9904-0.88850.03794.3145-1.8696-2.068-0.95961.59210.5548-0.21931.85020.17653.0173-61.108695.5202154.1668
173.44444.5306-4.19985.9961-5.33886.39520.83181.5387-1.07312.549-1.50233.4345-4.0506-2.8970.80532.22660.87070.10581.9887-0.18822.5202-65.932593.2981157.1586
182.67842.0217-1.32043.5009-4.99239.2938-0.05360.96140.49240.45770.0150.9927-0.3543-1.42170.06360.78060.206-0.02521.122-0.07981.6145-52.203676.0816155.1615
193.9739-0.62470.53591.71990.15842.0986-0.1777-1.17640.41450.86230.1522-0.4243-0.0750.29360.00310.98230.0404-0.12570.8798-0.17370.651-43.173828.697398.2157
204.7328-1.7228-0.1284.29070.55131.14160.19950.25850.65210.1473-0.0635-0.0455-0.4804-0.093-0.11670.72660.0490.14850.5017-0.01350.5373-62.065840.190172.4899
214.2354-0.5593-2.00184.30790.25354.01970.4909-0.14680.7378-0.3369-0.316-0.8108-0.32610.5308-0.15030.57480.0499-0.04310.6517-0.02661.0048-25.607625.848470.1304
222.7946-0.0084-0.1088-0.01840.36490.62220.78160.71250.8906-1.1591-0.2164-0.236-0.693-0.1814-0.3391.80970.39710.38471.00060.4441.1504-35.124344.364250.949
239.0911-5.2143-0.07323.1765-1.13979.1904-0.4907-0.26193.0069-1.30540.29640.4354-0.83490.24030.11861.1483-0.28360.07960.9311-0.04471.7642-27.864141.201170.3485
245.43040.60493.2621.2586-1.84816.0676-1.53410.37110.7290.5434-0.7193-0.8103-2.00241.28550.68712.9038-0.12441.33620.49150.99873.65-25.523858.17358.6449
257.65753.53171.89935.45074.65594.23740.3953-0.75071.63790.4346-0.3625-0.4563-0.5832.5542-0.03291.8583-0.25450.41511.38930.36042.1329-26.065550.885563.0889
263.0703-0.3446-1.17182.13880.4942.0976-0.04311.252-0.8168-0.6746-0.1340.10070.9107-0.48030.16181.1549-0.1196-0.04620.9225-0.27650.715210.629751.669266.2713
274.149-0.6539-2.63911.7252-0.2676.2473-0.2296-0.5626-0.1406-0.00830.16220.01390.79710.24990.05240.5181-0.0011-0.05390.4949-0.06290.459911.943861.784296.4113
283.4878-1.07410.3711.4864-1.08011.6023-0.1912-0.45190.87560.41890.1848-0.6641-0.01350.03540.00821.00450.230.0180.7345-0.22331.087143.210266.203783.1529
294.3075.89914.08559.59575.44123.8899-1.1039-2.76462.19461.44480.23711.37150.4108-1.12480.75381.06840.23180.13961.0062-0.191.174739.158454.73979.9601
305.3587-4.8603-5.6944.33725.12076.0086-1.18310.4522-1.4071.21910.9361.59060.7853-0.10240.33041.22220.3009-0.09241.5167-0.10781.438254.331445.720695.8997
314.31630.0753-5.08352.18610.4166.0993-2.1065-4.5927-0.28773.47490.6818-1.83640.88034.4461.39342.26440.7353-0.16912.64930.04341.769362.563242.80998.0788
327.80824.5120.37425.2988-2.38972.7099-0.6474-0.3124-0.5823-0.1830.155-0.1550.38320.55270.42421.0850.44450.06961.0862-0.17640.81445.357254.063690.0454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 338 through 555 )A338 - 555
2X-RAY DIFFRACTION2chain 'A' and (resid 556 through 694 )A556 - 694
3X-RAY DIFFRACTION3chain 'A' and (resid 695 through 792 )A695 - 792
4X-RAY DIFFRACTION4chain 'A' and (resid 793 through 860 )A793 - 860
5X-RAY DIFFRACTION5chain 'A' and (resid 861 through 912 )A861 - 912
6X-RAY DIFFRACTION6chain 'A' and (resid 913 through 1055 )A913 - 1055
7X-RAY DIFFRACTION7chain 'A' and (resid 1056 through 1196 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 8 )B4 - 8
9X-RAY DIFFRACTION9chain 'B' and (resid 9 through 18 )B9 - 18
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )C1 - 5
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 13 )C6 - 13
12X-RAY DIFFRACTION12chain 'D' and (resid 338 through 565 )D338 - 565
13X-RAY DIFFRACTION13chain 'D' and (resid 566 through 779 )D566 - 779
14X-RAY DIFFRACTION14chain 'D' and (resid 780 through 1204 )D780 - 1204
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 12 )E4 - 12
16X-RAY DIFFRACTION16chain 'E' and (resid 13 through 18 )E13 - 18
17X-RAY DIFFRACTION17chain 'F' and (resid 1 through 6 )F1 - 6
18X-RAY DIFFRACTION18chain 'F' and (resid 7 through 13 )F7 - 13
19X-RAY DIFFRACTION19chain 'G' and (resid 338 through 554 )G338 - 554
20X-RAY DIFFRACTION20chain 'G' and (resid 555 through 781 )G555 - 781
21X-RAY DIFFRACTION21chain 'G' and (resid 782 through 1018 )G782 - 1018
22X-RAY DIFFRACTION22chain 'G' and (resid 1019 through 1200 )G0
23X-RAY DIFFRACTION23chain 'H' and (resid 4 through 9 )H4 - 9
24X-RAY DIFFRACTION24chain 'H' and (resid 10 through 15 )H10 - 15
25X-RAY DIFFRACTION25chain 'I' and (resid 4 through 13 )I4 - 13
26X-RAY DIFFRACTION26chain 'J' and (resid 338 through 554 )J338 - 554
27X-RAY DIFFRACTION27chain 'J' and (resid 555 through 793 )J555 - 793
28X-RAY DIFFRACTION28chain 'J' and (resid 794 through 1197 )J794 - 1197
29X-RAY DIFFRACTION29chain 'K' and (resid 4 through 8 )K4 - 8
30X-RAY DIFFRACTION30chain 'K' and (resid 9 through 18 )K9 - 18
31X-RAY DIFFRACTION31chain 'L' and (resid 1 through 5 )L1 - 5
32X-RAY DIFFRACTION32chain 'L' and (resid 6 through 13 )L6 - 13

+
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