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- PDB-4ag6: Structure of VirB4 of Thermoanaerobacter pseudethanolicus -

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Basic information

Entry
Database: PDB / ID: 4ag6
TitleStructure of VirB4 of Thermoanaerobacter pseudethanolicus
ComponentsTYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
KeywordsHYDROLASE / TYPE IV SECRETION / CONJUGATION
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Helix Hairpins - #2170 / Helicase, Ruva Protein; domain 3 - #730 / TraG, P-loop domain / TraG P-loop domain / Helix Hairpins / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Helix Hairpins - #2170 / Helicase, Ruva Protein; domain 3 - #730 / TraG, P-loop domain / TraG P-loop domain / Helix Hairpins / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type IV secretory pathway VirB4 components-like protein
Similarity search - Component
Biological speciesTHERMOANAEROBACTER PSEUDETHANOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsWallden, K. / Williams, R. / Yan, J. / Lian, P.W. / Wang, L. / Thalassinos, K. / Orlova, E.V. / Waksman, G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
Authors: Karin Walldén / Robert Williams / Jun Yan / Pei W Lian / Luchun Wang / Konstantinos Thalassinos / Elena V Orlova / Gabriel Waksman /
Abstract: Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer ...Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S system is essential for both the assembly of the system and substrate transfer. In this article, we present the crystal structure of the C-terminal domain of Thermoanaerobacter pseudethanolicus VirB4. This structure is strikingly similar to that of another T4S ATPase, VirD4, a protein that shares only 12% sequence identity with VirB4. The VirB4 domain purifies as a monomer, but the full-length protein is observed in a monomer-dimer equilibrium, even in the presence of nucleotides and DNAs. We also report the negative stain electron microscopy structure of the core complex of the T4S system of the Escherichia coli pKM101 plasmid, with VirB4 bound. In this structure, VirB4 is also monomeric and bound through its N-terminal domain to the core's VirB9 protein. Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer.
History
DepositionJan 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
B: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
C: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
D: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,65413
Polymers177,7894
Non-polymers8659
Water4,702261
1
A: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
D: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1835
Polymers88,8952
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-42.8 kcal/mol
Surface area24890 Å2
MethodPISA
2
B: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
C: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4718
Polymers88,8952
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-71.6 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.286, 112.765, 156.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

21A-2058-

HOH

31A-2079-

HOH

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Components

#1: Protein
TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN / VIRB4 ATPASE


Mass: 44447.320 Da / Num. of mol.: 4 / Fragment: ATPASE DOMAIN, RESIDUES 203-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOANAEROBACTER PSEUDETHANOLICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: B0KAW2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 30% PEG 3350; 100 MM BIS-TRIS, PH 5.75; 200 MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9808
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9808 Å / Relative weight: 1
ReflectionResolution: 2.35→19.96 Å / Num. obs: 80446 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 39.26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SOLVERESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.35→19.956 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 3917 5 %
Rwork0.2262 --
obs0.2282 78167 96.46 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.239 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6384 Å20 Å20 Å2
2---0.3566 Å20 Å2
3----6.2818 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8854 0 45 261 9160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149424
X-RAY DIFFRACTIONf_angle_d1.10712360
X-RAY DIFFRACTIONf_dihedral_angle_d15.9223123
X-RAY DIFFRACTIONf_chiral_restr0.0761431
X-RAY DIFFRACTIONf_plane_restr0.0051591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.43390.31243440.25536961X-RAY DIFFRACTION91
2.4339-2.53110.29753680.24137102X-RAY DIFFRACTION93
2.5311-2.64610.26053820.23037217X-RAY DIFFRACTION95
2.6461-2.78520.30473740.23287366X-RAY DIFFRACTION96
2.7852-2.95920.29323570.23577513X-RAY DIFFRACTION97
2.9592-3.18680.27064180.22077514X-RAY DIFFRACTION99
3.1868-3.5060.26844160.22187628X-RAY DIFFRACTION99
3.506-4.00970.24264420.20737636X-RAY DIFFRACTION99
4.0097-5.03840.23074130.20177721X-RAY DIFFRACTION99
5.0384-19.95660.28844030.25657592X-RAY DIFFRACTION95
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)
11.688-2.15160.22736.6987-1.35781.13390.2706-0.5505-0.56-0.3356-0.02850.93160.57790.13350.01650.36390.06030.05580.21590.06850.4161-1.4292-39.5619-8.8957
20.0584-0.3877-0.26162.69291.40931.5902-0.0665-0.1061-0.1170.21410.01460.30580.2146-0.05450.03590.1440.03250.02080.12810.00230.1615-1.2341-20.2538-6.9354
30.354-1.05930.12873.15-0.28790.0306-0.28570.32030.0791-0.36430.3145-0.87560.3176-0.0918-0.17940.3167-0.00650.18820.2316-0.05660.543119.3451-3.6701-16.3867
44.1078-1.3416-2.46964.1677-0.82132.38950.06270.73850.6363-0.8740.2796-0.4273-0.271-0.3754-0.26790.3697-0.00030.13440.2944-0.01080.323110.3761-0.1352-24.8772
53.29981.7668-0.47941.5401-0.74081.5361-0.28010.1312-0.1057-0.19060.2783-0.1135-0.51980.0993-0.02910.3276-0.07910.13940.1974-0.04250.242316.38138.4082-20.096
60.2614-0.0292-0.87221.5297-0.31252.38620.0108-0.02180.0388-0.12310.2827-0.1871-0.3448-0.3347-0.17470.1792-0.00060.01550.15620.00140.15583.789-5.3854-12.4371
70.180.9688-0.02539.1914-2.92984.6393-0.42470.01910.86670.20190.4415-2.15920.1750.79580.13880.2864-0.0151-0.05610.3320.0080.932917.7529-14.6434-6.7354
80.93660.6298-0.37942.0420.34740.6967-0.0640.1540.0575-0.43880.1102-0.0485-0.10430.01170.01040.17970.05010.00330.1008-0.02630.11092.0877-18.5289-22.104
92.2201-0.46621.3633.038-1.32051.37290.2296-0.0724-0.4257-0.62120.08160.47220.1583-0.2958-0.30460.1194-0.0172-0.09060.11290.01680.1948-10.012-31.2628-18.2892
103.5948-0.97540.82711.8228-1.98882.30480.3093-0.72060.6184-0.12770.24340.18560.8258-0.5114-0.32240.8311-0.1250.13980.7110.01150.6134-10.9574-22.3943.6791
110.6365-0.208-0.02860.43780.13250.8935-0.248-0.1055-0.5327-0.27240.09850.16370.43110.0340.20170.65390.13080.11230.2885-0.02680.24811.4689-32.7775-64.5212
120.93790.56910.30480.25350.6672.43520.05120.119-0.2311-0.00040.0186-0.050.7520.19760.00310.42680.04050.06720.1007-0.0120.1975-1.2066-21.4909-61.8231
130.8586-0.37380.26520.44340.16380.76540.31670.2834-0.1265-0.24450.0552-0.2750.06010.0914-0.16270.31750.01180.10440.262-0.04130.2567-0.6288-8.0529-69.3071
141.18260.412-0.04110.88840.30030.21660.04760.0283-0.23930.2306-0.10980.00390.04970.00740.03470.1548-0.04080.08470.062-0.04530.1481-19.98290.1419-57.0614
152.3011-0.2676-0.45051.25610.67290.44170.2135-0.0594-0.17690.184-0.2380.00340.3356-0.05520.0540.25240.02040.05380.22120.00260.2082-24.06038.6852-49.922
162.73990.5277-1.98640.7752-0.07352.59390.18380.42250.4125-0.3288-0.058-0.1337-0.5601-0.3281-0.13350.27510.04550.04990.14820.01540.2034-19.546612.4078-56.2842
171.0392-0.9157-0.27742.13570.02710.71480.0568-0.00870.1165-0.22710.03360.1929-0.14870.0441-0.11160.2148-0.02760.06780.1037-0.03440.1243-8.9217-4.1262-62.4873
180.8984-0.4626-0.30521.2817-0.15361.1303-0.1594-0.109-0.02820.34870.07080.1207-0.00160.15840.1130.2524-0.03310.07730.0884-0.01350.1296-9.2299-12.4022-52.1297
190.98050.6338-0.74081.86461.91874.06530.0926-0.23390.2180.616-0.14270.06870.94310.75690.04320.47140.09890.04710.27240.05630.18130.5698-23.5163-47.3458
202.1009-0.27640.73681.70991.33351.40690.10060.5328-0.8460.57580.3942-0.37240.84940.7474-0.46210.41780.308-0.03650.4782-0.10880.16437.6532-27.269-56.1999
211.1678-0.3943-0.9570.33970.60790.9301-1.0337-0.9301-0.66430.44260.35290.12670.56990.32080.53710.4650.22990.35510.72670.18480.5329-42.64055.7729-29.8119
222.4797-0.4785-2.14030.71230.95723.5739-0.36150.0403-0.17160.1880.03250.2138-0.171-0.2030.04130.25870.06650.19190.4186-0.0450.3734-38.40887.1786-42.8022
234.0375-2.5967-1.95411.79031.35741.8428-0.73520.7385-1.30180.3879-0.36330.96950.6164-1.08990.84910.4034-0.23570.37580.8121-0.22580.7342-47.18672.2768-40.575
241.7441-0.4375-2.98990.13740.86568.21620.22630.2364-0.888-0.10130.76680.280.0543-0.04-0.39910.9671-0.19280.63120.50350.31191.611-49.762-8.1822-32.6163
252.9449-1.7851-0.34142.0784-1.22793.4018-2.118-1.7705-1.09470.8010.81350.75510.85850.63290.74690.71930.52720.52790.910.32320.6315-38.77480.6615-25.5261
261.7444-0.5239-1.19460.5332-0.10821.4338-1.2692-0.2581-1.41840.34610.235-0.18661.34250.75731.02721.42380.60331.14420.80060.51811.3282-34.9703-9.2351-31.8378
276.4862-2.77281.85754.5835-5.44646.8949-0.0963-2.1558-0.42152.2092-0.7199-0.4488-1.676-0.27590.64851.60910.5960.34551.70830.2650.475-26.78891.7922-20.2822
280.98990.5731-0.77280.317-0.41411.6713-0.7269-1.2634-0.66880.570.3596-0.2611-0.45730.23080.02861.03860.88680.48611.13090.36910.4896-31.5277-6.4212-21.4421
295.524-1.6524-0.88150.73360.32160.16480.0025-0.14591.4571-0.3776-0.8216-0.9672-0.2956-0.4290.07710.70320.80580.14371.762-0.020.8047-26.9712-11.0479-20.1546
300.0181-0.0074-0.01040.07210.08550.0973-0.1615-0.2486-0.24471.0198-0.28370.09051.19090.43250.2871.53230.09670.39310.54090.28660.9262-29.1237-24.354-20.1383
312.99860.0052-0.9510.7633-1.12632.25290.8227-0.96820.85570.2327-0.88210.52330.31971.1440.10910.3501-0.30.25431.836-0.58480.335946.23622.5339-48.9603
324.70441.90331.69751.2519-1.11577.1506-0.6263.3758-0.74750.31430.4334-0.4935-0.5191.61670.21090.5026-0.25330.23841.4126-0.26580.668231.73926.4464-40.5829
331.59421.2724-1.99482.1516-1.21872.64550.16170.82820.3699-0.61651.1596-0.2403-0.3244-0.3088-0.65460.4271-0.6280.25571.8342-0.44980.43726.35723.5988-38.7395
342.6073-0.75230.00880.56790.50942.4425-1.35821.6264-0.9572-0.0201-0.24710.6407-0.97250.31360.2662-0.0537-0.28320.80791.1086-0.40710.651232.85450.3771-30.6038
354.14451.4551-1.09191.1401-0.97021.5533-1.03040.65-0.2251-0.12481.1431-0.4367-0.1502-0.9434-0.14670.3976-0.51870.27831.4009-0.37660.574134.857910.4122-34.347
360.24650.35190.29280.39870.46840.4657-0.38960.7283-1.5931-0.22990.8294-1.40880.00341.2133-0.24220.3227-0.16450.45111.0779-0.53291.363642.801-1.0304-28.8671
372.2838-0.694-0.49442.056-0.79012.12850.566-0.5091-0.2361-1.6878-0.0861-0.1962-0.30621.3921-0.030.2075-0.25170.36690.8987-0.17750.427537.724-3.4869-49.8394
382.47590.9548-0.56572.972-0.30950.1765-0.33110.2336-1.1180.31660.25780.5581-0.26810.0310.0720.876-0.04130.25310.79620.11941.32826.7441-8.5424-46.2027
390.2119-0.5971-0.15562.39351.14761.06950.31650.0029-0.11940.3823-0.24130.69640.11580.28770.03380.9827-0.18520.00320.819-0.10310.933323.5246-3.3893-57.8845
401.4540.03371.55922.91941.78663.5542-0.90330.13510.4487-1.32740.53670.3691-0.8310.36310.02411.1189-0.3072-0.26310.781-0.49151.509532.5872-13.0741-57.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 204:210)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 211:298)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 299:326)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 327:338)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 339:421)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 422:457)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 458:463)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 464:547)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 548:582)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 583:587)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 204:229)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 230:262)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 263:292)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 293:337)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 338:361)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 362:421)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 422:464)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 465:522)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 523:555)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 556:583)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 286:318)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 319:387)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 388:430)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 431:442)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 443:472)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 473:490)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 491:498)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 499:517)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 518:533)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 540:548)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 287:299)
32X-RAY DIFFRACTION32(CHAIN D AND RESID 300:318)
33X-RAY DIFFRACTION33(CHAIN D AND RESID 319:330)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 331:361)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 362:387)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 388:416)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 417:473)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 474:491)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 492:501)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 502:536)

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