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- PDB-2ijx: Crystal structure of PCNA3 monomer from Sulfolobus solfataricus. -

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Basic information

Entry
Database: PDB / ID: 2ijx
TitleCrystal structure of PCNA3 monomer from Sulfolobus solfataricus.
ComponentsDNA polymerase sliding clamp A
KeywordsDNA BINDING PROTEIN / PCNA3 subunit / protein-protein interaction / PCNA123 heterotrimer
Function / homology
Function and homology information


leading strand elongation / DNA polymerase processivity factor activity / regulation of DNA replication / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 3
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHlinkova, V. / Ling, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.
Authors: Hlinkova, V. / Xing, G. / Bauer, J. / Shin, Y.J. / Dionne, I. / Rajashankar, K.R. / Bell, S.D. / Ling, H.
History
DepositionOct 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Aug 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 / pdbx_struct_special_symmetry / struct_ncs_dom_lim / 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_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: DNA polymerase sliding clamp A
B: DNA polymerase sliding clamp A
C: DNA polymerase sliding clamp A
D: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,19824
Polymers109,9564
Non-polymers1,24120
Water9,638535
1
A: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6754
Polymers27,4891
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7996
Polymers27,4891
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9869
Polymers27,4891
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7375
Polymers27,4891
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.773, 85.773, 264.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-642-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21B
31A
41C
12D
22B
32A
42C
13D
23B
33A
43C
14D
24B
34A
44C
15D
25B
35A
45C

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTYRTYRDD4 - 594 - 59
21VALVALTYRTYRBB4 - 594 - 59
31VALVALTYRTYRAA4 - 594 - 59
41VALVALTYRTYRCC4 - 594 - 59
12GLUGLUTYRTYRDD64 - 7364 - 73
22GLUGLUTYRTYRBB64 - 7364 - 73
32GLUGLUTYRTYRAA64 - 7364 - 73
42GLUGLUTYRTYRCC64 - 7364 - 73
13LYSLYSILEILEDD84 - 9984 - 99
23LYSLYSILEILEBB84 - 9984 - 99
33LYSLYSILEILEAA84 - 9984 - 99
43LYSLYSILEILECC84 - 9984 - 99
14PHEPHESERSERDD128 - 144128 - 144
24PHEPHESERSERBB128 - 144128 - 144
34PHEPHESERSERAA128 - 144128 - 144
44PHEPHESERSERCC128 - 144128 - 144
15VALVALPHEPHEDD174 - 228174 - 228
25VALVALPHEPHEBB174 - 228174 - 228
35VALVALPHEPHEAA174 - 228174 - 228
45VALVALPHEPHECC174 - 228174 - 228

NCS ensembles :
ID
1
2
3
4
5
DetailsThe biological assembly is monomer

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Components

#1: Protein
DNA polymerase sliding clamp A / Proliferating cell nuclear antigen homolog A / PCNA A


Mass: 27489.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnA, pcnA-1 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: P57765
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% PEG 3350, 0.15 M NH4Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: Si(111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 75947 / Num. obs: 75947 / % possible obs: 96.3 % / Redundancy: 23.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 32.2
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / % possible all: 65.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UD9
Resolution: 1.9→29.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.842 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 1530 2 %RANDOM
Rwork0.20401 ---
obs0.20493 74272 100 %-
all-75802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.162 Å0.177 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 80 535 8351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227964
X-RAY DIFFRACTIONr_bond_other_d0.0030.027383
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.98110712
X-RAY DIFFRACTIONr_angle_other_deg1.096317284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68125.947375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.974151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6181532
X-RAY DIFFRACTIONr_chiral_restr0.1180.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028719
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021477
X-RAY DIFFRACTIONr_nbd_refined0.2150.21408
X-RAY DIFFRACTIONr_nbd_other0.1880.27329
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23798
X-RAY DIFFRACTIONr_nbtor_other0.0880.25012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.271
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.2227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.56371
X-RAY DIFFRACTIONr_mcbond_other0.351.51993
X-RAY DIFFRACTIONr_mcangle_it1.39327956
X-RAY DIFFRACTIONr_scbond_it2.50533464
X-RAY DIFFRACTIONr_scangle_it3.5824.52747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D333tight positional0.120.05
12B333tight positional0.090.05
13A333tight positional0.160.05
14C333tight positional0.130.05
21D59tight positional0.060.05
22B59tight positional0.060.05
23A59tight positional0.10.05
24C59tight positional0.070.05
31D95tight positional0.080.05
32B95tight positional0.070.05
33A95tight positional0.110.05
34C95tight positional0.080.05
41D95tight positional0.080.05
42B95tight positional0.110.05
43A95tight positional0.070.05
44C95tight positional0.060.05
51D320tight positional0.080.05
52B320tight positional0.10.05
53A320tight positional0.080.05
54C320tight positional0.10.05
11D563loose positional0.925
12B563loose positional0.925
13A563loose positional1.35
14C563loose positional0.95
21D95loose positional0.815
22B95loose positional0.75
23A95loose positional1.045
24C95loose positional0.695
31D137loose positional0.725
32B137loose positional0.545
33A137loose positional0.545
34C137loose positional0.555
41D101loose positional0.635
42B101loose positional0.65
43A101loose positional0.695
44C101loose positional0.965
51D487loose positional0.735
52B487loose positional0.725
53A487loose positional0.935
54C487loose positional0.645
11D333tight thermal0.240.5
12B333tight thermal0.290.5
13A333tight thermal0.270.5
14C333tight thermal0.240.5
21D59tight thermal0.20.5
22B59tight thermal0.190.5
23A59tight thermal0.240.5
24C59tight thermal0.190.5
31D95tight thermal0.190.5
32B95tight thermal0.20.5
33A95tight thermal0.230.5
34C95tight thermal0.240.5
41D95tight thermal0.140.5
42B95tight thermal0.210.5
43A95tight thermal0.230.5
44C95tight thermal0.180.5
51D320tight thermal0.210.5
52B320tight thermal0.210.5
53A320tight thermal0.240.5
54C320tight thermal0.160.5
11D563loose thermal1.4410
12B563loose thermal1.7810
13A563loose thermal1.4610
14C563loose thermal1.4810
21D95loose thermal0.9110
22B95loose thermal1.3210
23A95loose thermal0.9810
24C95loose thermal0.8310
31D137loose thermal1.0910
32B137loose thermal0.7710
33A137loose thermal1.1110
34C137loose thermal0.8510
41D101loose thermal0.810
42B101loose thermal0.7910
43A101loose thermal0.9510
44C101loose thermal1.0110
51D487loose thermal1.1710
52B487loose thermal1.1310
53A487loose thermal1.3810
54C487loose thermal1.2710
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 87 -
Rwork0.2 4026 -
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)
13.8772.0257-1.09444.0274-1.13742.5954-0.1073-0.0132-0.2138-0.1744-0.0267-0.1542-0.0960.22630.1341-0.14430.00270.0677-0.14940.0451-0.123467.447750.473-409.3879
22.73130.5896-1.04271.2429-0.77524.72360.00770.27890.0338-0.0426-0.0020.04010.1974-0.1193-0.0058-0.2377-0.0308-0.0314-0.0710.056-0.195140.531725.064-383.0894
31.13640.65350.75732.78361.08415.80770.1078-0.1995-0.00940.1155-0.11130.0331-0.0879-0.20870.0035-0.1428-0.00020.0536-0.17140.053-0.163267.53224.1938-414.8038
44.25570.87690.60022.0050.53043.4506-0.1330.24330.3239-0.03170.07130.1037-0.0377-0.01890.0617-0.195-0.0161-0.0398-0.10790.0993-0.068685.997525.2004-381.4215
522.28874.15172.45392.87351.08283.9089-0.0824-0.56240.23780.2129-0.0967-0.1133-0.35730.31610.179-0.0805-0.0382-0.0121-0.16270.0928-0.215166.243459.3466-406.0098
64.02680.7064-0.409626.70153.42455.34330.3030.4565-0.1659-0.1232-0.4510.12980.172-0.35610.1479-0.274-0.0444-0.03990.02520.0447-0.221332.0625.4356-387.3471
77.6927-3.1396-0.59358.80820.90952.907-0.002-0.36070.28090.923-0.32570.22130.0389-0.43770.3277-0.0956-0.07340.0499-0.08170.0288-0.214964.1365-3.7176-411.1256
85.6726-4.6142.706713.1122-4.92365.8310.04520.39620.2432-0.407-0.23290.3792-0.27330.12770.1877-0.2261-0.0815-0.0603-0.0380.1014-0.116694.312628.1349-384.9224
96.25182.27692.25678.05956.649217.4878-0.08160.16680.0206-0.5280.0575-0.4189-0.67470.41460.0241-0.0753-0.026-0.0176-0.13350.0787-0.166170.830262.791-414.8383
106.5633.18147.09373.27164.793318.23620.10670.142-0.1119-0.1591-0.19240.41010.3023-1.05160.0857-0.2007-0.0447-0.04830.0047-0.0195-0.148227.525621.685-378.6142
118.82425.7622-13.20815.8692-6.598921.7181-0.1084-0.052-0.1098-0.0639-0.07480.39880.6023-0.56410.1832-0.14530.00690.052-0.06510.055-0.144459.1647-6.5019-420.0165
124.26051.3504-5.62425.9909-6.092124.08580.2152-0.09690.49830.0844-0.07850.0887-0.87710.2723-0.1368-0.17030.0003-0.0787-0.0640.06070.002996.469433.9282-376.5277
136.3793-0.8583-2.31875.9411-2.40765.8609-0.23640.4398-0.2143-1.05510.1751-0.12320.6993-0.22820.06130.1076-0.0820.0907-0.2018-0.0707-0.088759.336531.7661-414.4809
143.7557-0.61280.83163.4164-0.8633.9752-0.02750.04020.07820.24530.1444-0.02230.00430.1496-0.1169-0.2679-0.0101-0.042-0.16150.0125-0.192258.867434.5049-377.7123
157.3226-0.541-1.27952.5263-0.580.6410.11090.35260.22560.0760.07-0.0931-0.09110.053-0.1809-0.1056-0.00510.0643-0.19860.083-0.097783.484517.8055-418.8518
165.6955-3.46220.56137.3744-0.31125.5107-0.1669-0.2348-0.15760.53730.0756-0.0732-0.1538-0.18650.0913-0.2349-0.0745-0.0175-0.15740.0544-0.132572.009810.2256-375.8458
172.86610.8639-1.18915.4817-1.72455.5741-0.17240.1495-0.4254-0.7170.0879-0.12740.60270.08160.0845-0.0205-0.00620.1001-0.1853-0.0156-0.092560.258431.3671-411.622
184.37530.397-0.98692.50870.36872.76290.02260.04920.17870.21310.1196-0.29090.15440.1385-0.1422-0.22150.0304-0.0171-0.15490.029-0.181159.488933.1222-380.202
193.78391.26921.22973.7780.32382.3091-0.02830.15340.477-0.0921-0.0461-0.1588-0.34770.0430.0744-0.0910.03240.0743-0.18880.0482-0.074882.260718.8093-416.3338
203.88261.04650.36684.11480.75343.4907-0.0289-0.04920.01150.1899-0.09550.2140.0727-0.29720.1244-0.2187-0.0109-0.0091-0.10470.0435-0.124971.264410.8101-378.6616
2115.3142-6.6644-2.42769.1845-1.04966.7026-0.45910.3137-1.0822-0.62260.18270.81320.7392-0.42370.27640.192-0.09350.0614-0.0683-0.0339-0.034251.515926.3688-410.7573
223.1712-3.71721.96979.0674-3.69182.452-0.00450.27470.50760.0643-0.0797-0.7287-0.23830.26730.0842-0.17740.02340.0174-0.11170.0394-0.063364.442242.5136-381.7442
239.7285-4.34272.1214.2439-1.31362.53650.00440.01160.81720.2771-0.068-0.3862-0.46180.06460.0636-0.0429-0.02180.0419-0.18930.0115-0.013592.837219.8501-413.908
243.3586-5.19180.311511.02110.5050.88680.00540.2222-0.52690.2614-0.1240.25390.2134-0.39870.1186-0.1558-0.0422-0.0332-0.05630.031-0.079470.5546-0.1009-379.1384
2518.28537.6825-14.41596.5405-6.797216.6611-0.06190.4575-0.0064-0.30290.2902-0.270.0197-0.1991-0.2283-0.15920.04490.0983-0.2330.0117-0.126263.967138.712-407.6008
266.92995.1983-5.68768.7212-7.384610.81290.04860.14780.144-0.03230.31280.15940.1976-0.3867-0.3614-0.28450.0174-0.0482-0.13750.0363-0.241752.295628.9423-384.2795
2718.4673.267515.75054.26462.732220.337-0.21410.48010.1383-0.09660.1417-0.0743-0.37330.38880.0725-0.1277-0.00290.0774-0.24950.0327-0.184275.714212.6602-412.9583
283.4632-1.8619-1.251817.232112.665312.8451-0.16220.14040.00730.48440.14780.21890.40850.11870.0144-0.25490.00060.0072-0.1010.1063-0.158777.355616.7246-382.5973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 59
2X-RAY DIFFRACTION2B8 - 59
3X-RAY DIFFRACTION3C8 - 59
4X-RAY DIFFRACTION4D8 - 59
5X-RAY DIFFRACTION5A64 - 73
6X-RAY DIFFRACTION6B64 - 73
7X-RAY DIFFRACTION7C64 - 73
8X-RAY DIFFRACTION8D64 - 73
9X-RAY DIFFRACTION9A84 - 97
10X-RAY DIFFRACTION10B84 - 97
11X-RAY DIFFRACTION11C84 - 97
12X-RAY DIFFRACTION12D84 - 97
13X-RAY DIFFRACTION13A128 - 144
14X-RAY DIFFRACTION14B128 - 144
15X-RAY DIFFRACTION15C128 - 144
16X-RAY DIFFRACTION16D128 - 144
17X-RAY DIFFRACTION17A174 - 228
18X-RAY DIFFRACTION18B174 - 228
19X-RAY DIFFRACTION19C174 - 228
20X-RAY DIFFRACTION20D174 - 228
21X-RAY DIFFRACTION21A148 - 169
22X-RAY DIFFRACTION22B148 - 171
23X-RAY DIFFRACTION23C148 - 171
24X-RAY DIFFRACTION24D148 - 171
25X-RAY DIFFRACTION25A230 - 244
26X-RAY DIFFRACTION26B230 - 244
27X-RAY DIFFRACTION27C230 - 244
28X-RAY DIFFRACTION28D230 - 244

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